Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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Introduction
History of RNA biology
In 1958, Francis Crick established the central dogma of molecular biology by discovering the sequence of events in the passage of genetic material contained in DNA to the functioning of biological processes through proteins. However, with the development of new technologies and robust next-generation sequencing, large international consortiums such as the Functional Annotation of the Mammalian Genome (FANTOM) and the Encyclopaedia of DNA Elements (ENCODE) have described pervasive transcription (that 80% of the DNA is transcribed into RNA but only a 1.5% of that RNA translates into protein) (Carninci et al. 2005; Hangauer et al. 2013). Recent technological advances, like next-generation deep sequencing, have shown that the bulk of the genome is translated into RNAs. The universe of RNA is divided into two halves: (1) RNAs with coding potential and (2) RNAs without coding potential, sometimes known as non-coding RNAs, because of only 1 and 2% of the human genome codes for proteins (The ENCODE Project Consortium 2012). Although mRNAs have been studied in depth, most RNAs are ncRNAs. Even though ncRNAs were formerly regarded as “evolutionary junk,” new research shows that they substantially impact several molecular pathways. According to the hypothesis known as the “RNA universe,” RNA was the earliest form of life, and as DNA became more solid, RNA’s function as a messenger was left unfilled. However, it was eventually discovered that RNA is the most practical possibility in disease, epigenetics, and unknown regulatory features since it has a wide range of latent catalytic capabilities and can store genetic information (Bhatti et al. 2021). During evolution, RNA is thought to have evolved alongside proteins and DNA (Robertson and Joyce 2010). Understanding their intricate relevance in numerous biological processes, including homeostasis and development, is critical (Amaral et al. 2013). Figure 1 demonstrates the molecular events relate to non-coding RNA (Li et al. 2021a, b; Chhabra 2021).
A relatively broad size criterion is used to classify ncRNAs into two subclasses. Small or short non-coding RNAs (ncRNAs) are ncRNAs that are less than 200 nucleotides (nt), while long non-coding RNAs are ncRNAs that are more than 200 nt (lncRNAs). These two groups are quite different from one another. LncRNAs can be as significant as several kilobases, and small ncRNAs can be as small as a few to 200 nt. The most well-known class of tiny ncRNAs, microRNAs (miRNAs), have a length of 20 nucleotides or less and have undergone substantial research (Kim et al. 2009). The other non-coding such as siRNA and piRNA. The complexity of these animals’ physiology, characteristics, and development, from lower non-chordates to humans, produces an increase in introns and intergenic sequences that are translationally modified by alternative splicing processes, leading to a further decrease in the size of this proteome (Mattick 2001).In addition, eukaryotes have more sophisticated and complex systems for RNA processing, trans induction, DNA methylation, imprinting, RNA interference (RNAi), post-transcriptional gene silencing, chromatin modification, gene editing, splicing, dosage compensation, gene regulation mechanisms, and transcriptional gene silencing (Mattick 2004). Non-coding RNA act as regulatory signal messengers for the stimuli received at sensory genetic elements (Guttman et al. 2011). The evolutionary history of prokaryotes supports their continued reliance on protein-based regulatory architecture, in contrast to eukaryotes, who have evolved new regulatory features and mechanisms to control the expression of phenotypic traits, the penetrance and expressivity of disease, and developmental programming using a variety of ncRNAs. Therefore, research on ncRNA about these linked pathways is essential to comprehend their function in health and disease (GAGEN 2005).
Distribution and types of ncRNA
RNA comes in a variety of forms in live cells. ncRNAs are typically split into two domains based on their transcript length: short ncRNAs (under 200 nucleotides) and long ncRNAs (over 200 nucleotides). ncRNA is important in several processes, including RNA maturation, RNA processing, signaling, gene expression, and protein synthesis (Kung et al. 2013; Morris and Mattick 2014). The amount of ncRNA and the degree of species conservation are remarkably correlated. According to estimates, each cell has 107 ncRNA molecules, most of which are snRNA, snoRNA, miRNA, rRNA, and lncRNA. Although about 53,000 distinct human lncRNAs identified, only about 1000 are present in adequate quantities to legitimately support their functional significance (Djebali et al. 2012). Other types of RNA and their specificities are mentioned in this study (Bhatti et al. 2021). The overview of non-coding RNA and its functions is mentioned in Table 1. The different types of RNA are mentioned in Fig. 2.
Biogenesis and functions of different types of ncRNA
RNA molecules are much more than just a blueprint for protein production. Since non-coding transcripts are expected to function similarly to proteins and can regulate the majority of cellular functions, RNA may interact with DNA, proteins, and other RNA molecules to form three-dimensional (3D) structures. The two main regulatory RNA groups—small and long ncRNAs—are partly defined by their length. Additionally, functional ncRNAs with lengths between 20 and thousands of nucleotides have grown significantly in number and classification over the past ten years. This review focuses on significant ncRNAs such as miRNA, lncRNA, and circRNA. Few other RNA will be mentioned such as piRNA, snRNA, snoRNA, and siRNA. This ncRNA will play a significant role in developmental processes and disease conditions. Numerous genes are involved in the production of ncRNAs across the whole human genome, and there may potentially be distinct transcriptional units that function independently. Transcription, nuclear maturation, export to the cytoplasm for processing, and production of functional RNA are all steps in this biogenesis process. The detailed mechanism of non-coding RNA biogenesis is mentioned in this paper (Bhatti et al. 2021). The description of specific ncRNA and the description of biogenesis are mentioned in Table 2. Non-coding RNA is an integral part of genomics and proteomics. According to the “RNA world” hypothesis, RNA may have played a role in the emergence of life, which must be able to carry and duplicate its genetic material (Joyce 1989). In contemporary organisms that have evolved to use more effective methods to copy and express their genetic material along the central axis from DNA to RNA to protein, ncRNAs seem to have retained the majority, if not all, of their original characteristics and functions. Many RNA functions are transferred to proteins while others are kept because of the exploration of selective benefits of proteins and RNA during evolution. To grasp ncRNA function and mechanism, it may be instructive to compare ncRNA function with that of proteins.
Comparison of miRNA, lncRNA, and circRNA in RNA biology
The mechanistic characterization of lncRNAs is far less thorough than that of miRNAs. This is partly because lncRNAs can control gene expression through intricate biochemical pathways at various levels inside the cell. Despite being present in a group of species (Guttman and Rinn 2012), such as plants (Swiezewski et al. 2009), yeast (Houseley et al. 2008), prokaryotes (Bernstein et al. 1993), and viruses (Reeves et al. 2007), lncRNAs are not as well conserved as miRNAs in terms of the nucleotide sequence. Even though lncRNAs with diverse nucleotide compositions can exhibit the same 3D structure and, consequently, the exact molecular function, this restricts the selection of cellular and animal models for researching lncRNA functions (Derrien et al. 2012). It is increasingly becoming clear that lncRNAs play a role in virtually every cellular process and that the expression of these non-coding molecules is carefully regulated in both normal conditions and several human diseases, including cancer (Tano and Akimitsu 2012).
Unlike coding genes, lncRNAs can be produced in many ways from practically any location in the human genome. Contrary to those that overlap coding genes on the antisense strand, unlike coding genes, lncRNAs can be produced in a wide range of ways from practically any location in the human genome. Contrary to those that overlap coding genes on the antisense strand, sense lncRNAs are made from segments that overlap one or more exons of another coding transcript (antisense lncRNAs); sense lncRNAs are made from segments that overlap one or more exons of another coding transcript. Other lncRNAs are produced by regulatory components like enhancers or non-coding DNA sequences like introns. Some have promoters and regulatory elements expressed from intergenic regions that do not overlap other known coding genes (Thum and Condorelli 2015). It becomes clear that just a tiny portion of the theoretically infinite number of lncRNAs that could exist have been studied thus far. However, those studied have demonstrated the capacity to control the transcriptional and post-transcriptional stages of gene expression by interacting with nucleic acids and proteins in a manner that is specific to both sequences and structures (Mercer et al. 2009; Wilusz et al. 2009). The categorization and annotation of putative lncRNAs must be carefully examined to remove protein-coding RNAs. While being categorized as non-coding molecules, some lncRNAs have recently been shown to be able to code for micro peptides (Anderson et al. 2015). Before concluding a lncRNA’s regulatory role, it is essential to prove that the skeletal muscle-specific RNA, which was previously thought to be a lncRNA, is encoded for a functional micro peptide. Evidence from recent studies revealed that conventional processes do not just regulate ncRNA expression. Circular RNAs are produced due to a back-splicing expression variation (circRNA). Since CircRNAs are made up of a covalently closed continuous loop, they lack a 5′ cap and a 3′ tail. This RNA species is more tissue-specific, moderately stable, and highly conserved (Jeck et al. 2012). The functions of each of these ncRNA were mentioned in this paper (Beermann et al. 2016). The discovery of associations between non-coding RNAs and diseases has created new therapeutic and diagnostic possibilities. Numerous miRNAs have already been effectively demonstrated to act as diagnostic or therapeutic targets for various diseases. There is specific evidence that circRNAs and lncRNAs behave similarly.
Non-coding RNA and human diseases
Functional RNA molecules known as non-coding RNA (ncRNA) cannot be translated into proteins (Djebali et al. 2012). Initially, there are only a few ncRNAs were found and studied. Later technological advancements, ncRNA types were classified into many, and each ncRNA has specific functions that lead to biomarkers and novel therapeutic approaches. Despite not all of their functions being understood, several ncRNA species play crucial roles in controlling the transcription and translation of genes and the transcription of ncRNAs. Therefore, it is no surprise that ncRNAs are crucial in normal physiologic functions, complex human traits, and human diseases (Li et al. 2018a, b). This review will mention the different types of diseases and their ncRNA as potential biomarkers and interactions in Table 3.
Transposons: unexpected players in different diseases with different ncRNA
Transposable elements (TEs) are considered essential factors in the plasticity and evolution of the genome. Since TEs are so prevalent in the human genome, particularly the Alu and Long Interspersed Nuclear Element-1 (LINE-1) repeats, they are thought to be the molecular cause of several diseases. This encompasses a number of the molecular processes discussed in this article, including insertional mutation, DNA recombination, chromosomal rearrangements, changes in gene expression, and changes to epigenetic controls. Additionally, some of the more well-known and/or more recent cases of human disorders where TEs play a role are provided in this article (Chénais 2022). TEs are frequently linked to the genesis of human malignancies, whether through the insertion of LINE-1 or Alu elements that result in chromosomal rearrangements or epigenetic alterations. Numerous more clinical disorders may have their molecular roots in gene structure and/or expression changes or chromosomal recombination caused by TE. Hemoglobinopathies, metabolic, neurological, and joint disorders are among the many conditions this group of diseases represents.
Additionally, TEs may influence aging. The epigenetic derepression and mobility of TEs, which can result in disease development, appear to be significantly impacted by the pressures and environmental toxins that people are exposed to. As a result, a greater understanding of TEs may result in the development of novel possible disease diagnostic markers (Pradhan and Ramakrishna 2022).
Differences between exosomal and non-exosomal non-coding RNAs in human health and diseases
Circulating ncRNA transfer via exosomes is an intriguing method. As mediators for intercellular communication, ncRNAs can be enclosed by EVs (such as exosomes, microvesicles, and apoptotic bodies) and secreted from cells to control various diseases depending on the target cells (Li et al. 2021a). It has been demonstrated that ncRNAs exist in various bodily fluids, including serum, plasma, urine, saliva, and others, in addition to cells. The ncRNAs seen in biofluids are frequently called circulating or extracellular ncRNAs. The fact that extracellular ncRNAs are reasonably durable in plasma even though extracellular RNase activity is considerable in that environment suggests that circulating ncRNAs may be shielded from adverse circumstances. In this part, they examine how ncRNAs in exosomes and non-exosomes regulate physiological homeostasis and pathological events in health and disease (Li et al. 2021b).
Tools and methods
Investigating miRNA, lncRNA, circRNA, and other RNAs
The complete methods and investigation of ncRNA will be discussed. miRNA methods have already been thoroughly explained. Deep sequencing techniques or microarrays are the most used methods for miRNA detection. Deep sequencing is a more sensitive technique when compared to microarray-based techniques. Microarrays can lead to finding distinct RNA sequences despite using a fixed set of probes for detection (van Rooij 2011). However, the output analysis is more difficult because of the enormous volume of data and the critical requirement for bioinformatics expertise. Quantitative real-time PCR allows for the comparatively inexpensive and low-effort validation of screening results (qRT-PCR). Because the transcript is so brief, previous difficulties prompted the construction of the primer for reverse transcription. Target-specific stem-loop reverse transcription primers are currently offered on many platforms. Northern blotting and in situ hybridization are other techniques for identifying identified miRNAs. To find a miRNA’s targets, bioinformatics platforms are commonly implemented. The miRNA-related database is mentioned in Table 4. Luciferase tests are frequently used to verify expected targets of miRNAs following bioinformatics-based predictions of such targets. To completely comprehend the entire transcriptional regulatory scenario, small RNAs play a critical role in transcriptional regulation. Their abnormal expression profiles are believed to be linked to cellular dysfunction and diseases. Numerous studies are concentrating on detecting, predicting, or quantifying short RNA expression, particularly miRNAs, to better understand human health and disease.
The efficient and reasonably good next-generation sequencing approach allows the collection of large data sets with excellent accuracy. Appropriate bioinformatic procedures must be used to use the collected data and analyze for lncRNAs. Additionally, you can buy commercial arrays to look at the deregulation of a specific set of lncRNAs (e.g., Arraystar, Qiagen, Biocat). Another method to investigate the effect of lncRNAs is to use a genome-wide shRNA library to target a specific subset of lncRNAs. This library and additional studies might be used to ascertain how lncRNA inhibition influences signaling pathways or cell behavior. For instance, the lncRNA TUNA was discovered in mouse embryonic stem cells with Oct4-GFP using an shRNA library targeting 1280 lincRNA (Lin et al. 2014). The pros and cons of RNAi approaches are effectively summed up in a review written by Mohr et al. (Mohr et al. 2014).
Designing primers that only detect the ncRNA transcript is crucial for validating a screen’s results for lncRNAs. To identify coding from non-coding regions, this design is essential. A lncRNA often has modest levels of expression. In addition, lncRNA annotation is continuously evolving and may not be consistent across all databases (like Refseq, UCSC, and Ensembl). Since pseudogenes typically produce lncRNAs, the actual gene and the long non-coding transcript can be recognized using the same primers. Another difficulty arises when lncRNAs are expressed sense- or antisense-to a recognized protein-coding gene. LncRNAs are primarily found in cell nuclei. There are many challenges associated with pulling down lncRNA/protein complexes since it may provide false-positive outcomes. A highly reproducible RNA antisense purification (RAP) method was described in this paper (McHugh et al. 2015). In vitro, lncRNAs can be suppressed using a variety of compounds. It is also critical to confirm the length of annotated sequences for newly discovered lncRNAs. The rapid amplification of cDNA ends (RACE) method can amplify a lncRNA between a specific point inside the lncRNA and the sequence’s 3′ or 5′ end. The actual sequence can then be found or verified by cloning and sequencing this amplicon (Beermann et al. 2016). Detail-oriented loss- or gain-of-function studies are essential to comprehend a lncRNA’s activity in vivo (Bassett et al. 2014). Numerous lncRNA-related database was mentioned in Table 5.
By searching current RNA-sequencing data for circular RNAs, a brand-new set of probable circRNAs can be predicted (Salzman et al. 2012). Data from long-read RNA sequencing can be utilized to look for possible circRNAs. This particular class of molecules requires a specific algorithm because their production may have involved back-splicing. Two studies demonstrate how to build a computational pipeline to identify new circRNAs (Guo et al. 2014). Using these new techniques to analyze RNA-sequencing data provides suggestions for existing circRNAs. Because the gene from which they are derived has a distinct orientation, the validation of these ncRNAs is particularly unique. Exonic circRNAs must be separated from other RNA molecules that have undergone backspacing. Divergent primers can be used in qPCRs to access the expression and access the predicted circRNAs.
Regarding the genomic area, these primers do not amplify toward one another but are somewhat away from one another. The circle can be amplified without amplifying the genomic areas (Jeck and Sharpless 2014). The functional circRNA can be accessed through previous RNA studies, which are still evolving. Other new approaches should be implemented for the circRNA. New tools and approaches to small ncRNA and circRNA were mentioned in Tables 6 and 7.
Identifying non-coding RNAs (ncRNAs), which play a significant function in the cell, is a crucial topic in biological study. The discovery of ncRNAs is now conceivably feasible, thanks to recent developments in computational prediction technology and bioinformatics. This study introduces three key computational methods for ncRNA identification: homologous search, de novo prediction, and deep sequencing data mining. There are two methods for detecting the ncRNA identification Homologous information and machine learning approaches (i.e., common features)aforementioned computational detection techniques are mostly intended for short non-coding RNAs like miRNAs, tRNAs, siRNAs, and piRNAs. However, conventional methods like PT-PCR and Northern Blot are expensive. The calculation methods can never perform well when dealing with long non-coding RNAs (lncRNA). To the current knowledge, the primary lncRNA detection method is RT-PCR or CHIP-SEQ (Wang et al. 2013). The primary software tools and ncRNA discovery method tools are mentioned in Table 8. The techniques used for ncRNA discovery are mentioned in Table 9.
Applications of CRISPR/Cas9-mediated non-coding RNA editing in the targeted therapy of human diseases
Genome editing, also known as gene editing, refers to a range of scientific techniques that enable the modification of an organism’s DNA. These techniques enable adding, removing, or modifying genetic material at specific genomic regions. There are several genome editing methods, including ZFNs, TALENs, and CRISPR/Cas9. Comparison of these three approaches was mentioned in this article (Li et al. 2021a, b). The detailed structure and mechanism of these three different approaches were mentioned in this article (Li et al. 2021a, b).
CRISPR-Cas9, which stands for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9, is a well-known example. The CRISPR/Cas9 system has evolved and developed quickly as a reliable, practical, user-friendly, and widely applied gene editing tool in just a few years. CRISPR/Cas9 has significantly impacted a wide range of industries, including agriculture, biotech, and healthcare. However, no industry has been affected by the technology more profoundly than cancer research, as indicated by the accumulating data in the rapidly expanding publications. The discovery and application of more specific Cas9 variants, limiting the duration of CRISPR/Cas9 activity, the use of inducible Cas9 variants, and the application of anti-CRISPR proteins (Zhang et al. 2021a, b). Further research is required to fully comprehend the governing principles of CRISPR/Cas9 specificity and to increase the sensitivity of off-target identification. Second, on-target mutagenesis typically occurs in double-strand breaks brought on by single-guided RNA/Cas9, leading to massive deletions (over several kilobases) and complex genomic rearrangements at the targeted loci, which can have pathogenic effects (Zhang et al. 2021a, b).
The research evidence accumulated to date has shown significant contributions made by genome editing systems to exploit therapeutic approaches for various types of human diseases, with the CRISPR/Cas9 system being particularly successful by directly affecting target gene loci or generating tools with multiple functions. There are other diseases these approaches were found to therapeutic drugs of clinical drugs mentioned in this article (Li et al. 2021a, b). The advancement of cell imaging, gene expression regulation, epigenetic modification, therapeutic drug development, functional gene screening, and gene diagnosis has also been aided by gene editing technologies at the same time. Innovative genome editing complexes and more focused nanostructured vesicles have improved efficiency and reduced toxicity during the delivery process, bringing genome editing technology closer to the clinic. It is reasonable to assume that genome editing technology has the potential to ultimately elucidate biological mechanisms behind disease development and progression, providing novel therapies and ultimately promoting the development of the life sciences, with further investigation into this technology (Li et al. 2020; Li et al. 2021a, b).
Non-coding RNA therapeutics
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), as well as other types of non-coding RNAs (ncRNAs), are intriguing targets for therapeutic intervention in the treatment of cancer and a variety of other diseases. Many antisense oligonucleotides and small interfering RNAs have been used in the clinical use of RNA-based treatments over the past ten years, and several of these have acquired FDA approval. Trial findings, however, have been mixed up to this point, with some studies claiming strong effects and others showing minimal efficacy or toxicity. Clinical trials are being conducted on alternative entities like antimiRNAs, and interest is growing in lncRNA-based therapies (Winkle et al. 2021).In this review, the existing therapeutic RNA and clinical trial drugs will be mentioned in Table 10.
Challenges in using ncRNA as biomarkers and therapeutic targets
Non-coding RNAs may be potential biomarkers and therapeutic targets because mounting data suggests they are critical regulators of the pathophysiological processes leading to many diseases. However, its clinical use has not been examined and may face numerous difficulties. First, non-coding RNAs are still being developed as biomarkers. Although RT-PCR, next-generation sequencing, and microarray analysis have been utilized in research examining the connection between non-coding RNAs and disease-specific traits, most of these investigations are still experimental. However, no research has examined the viability of choosing lncRNA/circRNA as novel biomarkers (Zhang et al. 2017a, b). The discovery of tissue- or organ-specific biomarkers would be beneficial for the early diagnosis, treatment, and intervention of organ failure, perhaps increasing the chance of disease-specific survival.
Because they differ from conventional medications, such as small-molecule and protein medicines, which are also known to work primarily on protein targets, RNA-based therapies are considered the next generation of therapeutics. First, RNA aptamers can produce pharmacological effects by blocking the activity of a particular protein target. Second, for controlling a specific disease, antisense RNAs (asRNAs), miRNAs, and siRNAs can be created to specifically target mRNAs or functional ncRNAs. Thirdly, to cure a monogenic condition, gRNAs may be used to precisely alter the target sequences of a particular gene. Thus, RNA therapies can potentially increase the number of druggable targets. On-coding RNAs are promising “next-generation” biomarkers since the issues mentioned earlier and difficulties can be resolved. Non-coding RNAs may one day serve as innovative treatment targets with the help of a more profound knowledge of the mechanism underlying those specific diseases.
Conclusion and future perspectives
The attractive new field of ncRNA research demonstrates a higher level of nature’s diversity. The complexity of ncRNA research results from the more significant than specified based on ncRNAs in cellular biology. Nevertheless, even though ncRNAs have recently been discovered, there have been significant advancements in clinical applications and diagnostic methods. This research will likely expand into a new area of more potent and particular medications and personalized medicine techniques, elevating patient care to a new level. Rapid developments in bioinformatics, sequencing technologies, proteomics, and microarrays have identified a wide variety of non-coding RNAs (ncRNA), which comprise most cellular mechanism regulators principally linked to eukaryotic complexity. It seems more difficult to comprehend the unique function of these non-coding RNAs with these varied ncRNAs having integrated, complicated networks and biological pathways. The use of ncRNA therapies in formal drug development will increase.
Further information has to be obtained, possible ncRNA medicines’ pharmacokinetics and dynamics need to be examined, and thorough toxicological studies are required. To advance the field, more tools are required. There will be more phase I/II clinical studies. This study aims to investigate and advance knowledge of the mechanisms and functions of ncRNAs in human health and disease and to pave the way for novel clinical diagnostic and therapeutic approaches. When dealing with the enormous quantity of ncRNAs that need to be analyzed, ML outperforms since it can quickly address the fundamental problem. By categorizing healthy and disease samples, the current analysis of ncRNAs using ML demonstrates reasonable accuracy, indicating that the differentiation pattern is apparent in those instances. Therefore, future research should concentrate on increasing the likelihood that the ML models will recognize the distinctive pattern of each disease. However, the use of ncRNAs may significantly rise in the following years, which will contribute to the development of successful precision medicine and more individualized therapies.
Data availability
No supporting data is available in this study.
Code availability
Not applicable.
Abbreviations
- ncRNA:
-
Non-coding RNA
- lncRNA:
-
Long non-coding RNA
- miRNA:
-
MicroRNA
- circRNA:
-
Circular RNA
- snRNA:
-
Small nuclear RNA
- snoRNA:
-
Small nucleolar RNAs
- siRNA:
-
Small interfering RNA
- rRNA:
-
Ribosomal RNA
- piRNA:
-
PIWI-interacting RNA
- FANTOM:
-
Functional Annotation of the Mammalian Genome
- ENCODE:
-
Encyclopedia of DNA Elements
- Nt:
-
Nucleotide
References
Adams D, Gonzalez-Duarte A, O’Riordan WD, Yang C-C, Ueda M, Kristen AV, Tournev I, Schmidt HH, Coelho T, Berk JL, Lin K-P, Vita G, Attarian S, Planté-Bordeneuve V, Mezei MM, Campistol JM, Buades J, Brannagan TH, Kim BJ, Oh J (2018) Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis. N Engl J Med 379(1):11–21. https://doi.org/10.1056/nejmoa1716153
Agarwal V, Bell GW, Nam J-W, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. ELife 4. https://doi.org/10.7554/elife.05005
Ahadi A, Sablok G, Hutvagner G (2016) miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA–target interaction data. Nucleic Acids Res 45(6):e42–e42. https://doi.org/10.1093/nar/gkw1185
Ahmed F, Kaundal R, and Raghava GP (2013) PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC Bioinforma 14(S14). https://doi.org/10.1186/1471-2105-14-s14-s9
Ahmed M, Nguyen H, Lai T, Kim DR (2018) miRCancerdb: a database for correlation analysis between microRNA and gene expression in cancer. BMC Res Notes 11(1):103. https://doi.org/10.1186/s13104-018-3160-9
Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks JB, Kapfer C, Mineta K, Gojobori T, Bajic VB (2017) FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Res 45(5):2838–2848. https://doi.org/10.1093/nar/gkw973
Alon S, Erew M, Eisenberg E (2015) DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data. Bioinformatics 31(15):2568–2570. https://doi.org/10.1093/bioinformatics/btv187
Amaral PP, Dinger ME, Mattick JS (2013) Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective. Brief Funct Genomics 12(3):254–278. https://doi.org/10.1093/bfgp/elt016
Anderson DM, Anderson KM, Chang C-L, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, Olson EN (2015) A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance. Cell 160(4):595–606. https://doi.org/10.1016/j.cell.2015.01.009
Andrés-León E, González Peña D, Gómez-López G, Pisano DG (2015) miRGate: a curated database of human, mouse and rat miRNA–mRNA targets. Database 2015. https://doi.org/10.1093/database/bav035
Annese T, Tamma R, De Giorgis M, Ribatti D (2020) microRNAs biogenesis, functions and role in tumor angiogenesis. Front Oncol 10. https://doi.org/10.3389/fonc.2020.581007
Anttila V, Saraste A, Knuuti J, Jaakkola P, Hedman M, Svedlund S, Lagerström-Fermér M, Kjaer M, Jeppsson A, Gan L-M (2020) Synthetic mRNA Encoding VEGF-A in Patients Undergoing Coronary Artery Bypass Grafting: Design of a Phase 2a Clinical Trial. Mol Ther - Methods Clin Dev 18:464–472. https://doi.org/10.1016/j.omtm.2020.05.030
Aw JGA, Shen Y, Wilm A, Sun M, Lim XN, Boon K-L, Tapsin S, Chan Y-S, Tan C-P, Sim AYL, Zhang T, Susanto TT, Fu Z, Nagarajan N, Wan Y (2016) In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. Mol Cell 62(4):603–617. https://doi.org/10.1016/j.molcel.2016.04.028
Baden LR, El Sahly HM, Essink B (2020) Efficacy and safety of the mRNA-1273 SARS CoV-2 vaccine. N Engl J Med 384(5). https://doi.org/10.1056/nejmoa2035389
Bafna V, Zhang S (2004) FastR: fast database search tool for non-coding RNA. Proc IEEE Comput Syst Bioinform Conf 52–61. https://doi.org/10.1109/csb.2004.1332417
Ballabio E, Mitchell T, van Kester MS, Taylor S, Dunlop HM, Chi J, Tosi I, Vermeer MH, Tramonti D, Saunders NJ, Boultwood J, Wainscoat JS, Pezzella F, Whittaker SJ, Tensen CP, Hatton CSR, Lawrie CH (2010) MicroRNA expression in Sezary syndrome: identification, function, and diagnostic potential. Blood 116(7):1105–1113. https://doi.org/10.1182/blood-2009-12-256719
Ballarino M, Cazzella V, D’Andrea D, Grassi L, Bisceglie L, Cipriano A, Santini T, Pinnarò C, Morlando M, Tramontano A, Bozzoni I (2015) Novel long noncoding RNAs (lncRNAs) in myogenesis: a miR-31 overlapping lncRNA transcript controls myoblast differentiation. Mol Cell Biol 35(4):728–736. https://doi.org/10.1128/MCB.01394-14
Balloy V, Koshy R, Perra L, Corvol H, Chignard M, Guillot L, Scaria V (2017) Bronchial Epithelial Cells from Cystic Fibrosis Patients Express a Specific Long Non-coding RNA Signature upon Pseudomonas aeruginosa Infection. Front Cell Infect Microbiol 7:218. https://doi.org/10.3389/fcimb.2017.00218
Balwani M, Sardh E, Ventura P, Peiró PA, Rees DC, Stölzel U, Bissell DM, Bonkovsky HL, Windyga J, Anderson KE, Parker C, Silver SM, Keel SB, Wang J-D, Stein PE, Harper P, Vassiliou D, Wang B, Phillips J, Ivanova A (2020) Phase 3 Trial of RNAi Therapeutic Givosiran for Acute Intermittent Porphyria. N Engl J Med 382(24):2289–2301. https://doi.org/10.1056/nejmoa1913147
Ban J-J, Chung J-Y, Lee M, Im W, Kim M (2017) MicroRNA-27a reduces mutant hutingtin aggregation in an in vitro model of Huntington’s disease. Biochem Biophys Res Commun 488(2):316–321. https://doi.org/10.1016/j.bbrc.2017.05.040
Bandyopadhyay S, Mitra R (2009) TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 25(20):2625–2631. https://doi.org/10.1093/bioinformatics/btp503
Bañez-Coronel M, Porta S, Kagerbauer B, Mateu-Huertas E, Pantano L, Ferrer I, Guzmán M, Estivill X, Martí E (2012) A Pathogenic Mechanism in Huntington’s Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity. PLoS Genet 8(2):e1002481. https://doi.org/10.1371/journal.pgen.1002481
Bao Z, Yang Z, Huang Z, Zhou Y, Cui Q, Dong D (2018) LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res 47(D1):D1034–D1037. https://doi.org/10.1093/nar/gky905
Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP (2014) Considerations when investigating lncRNA function in vivo. ELife 3. https://doi.org/10.7554/elife.03058
Bauters C, Kumarswamy R, Holzmann A, Bretthauer J, Anker SD, Pinet F, Thum T (2013) Circulating miR-133a and miR-423-5p fail as biomarkers for left ventricular remodeling after myocardial infarction. Int J Cardiol 168(3):1837–1840. https://doi.org/10.1016/j.ijcard.2012.12.074
Bayes-Genis A, Voors AA, Zannad F, Januzzi JL, Mark Richards A, Díez J (2017) Transitioning from usual care to biomarker-based personalized and precision medicine in heart failure: call for action. Eur Heart J 39(30):2793–2799. https://doi.org/10.1093/eurheartj/ehx027
Bayoglu B, Yuksel H, Cakmak HA, Dirican A, Cengiz M (2016) Polymorphisms in the long non-coding RNA CDKN2B-AS1 may contribute to higher systolic blood pressure levels in hypertensive patients. Clin Biochem 49(10–11):821–827. https://doi.org/10.1016/j.clinbiochem.2016.02.012
Bedewy AML, Elmaghraby SM, Shehata AA, Kandil NS (2017) Prognostic Value of miRNA-155 Expression in B-Cell Non-Hodgkin Lymphoma. Turkish J Haematol 34(3):207–212. https://doi.org/10.4274/tjh.2016.0286
Beermann J, Piccoli M-T, Viereck J, Thum T (2016) Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. Physiol Rev 96(4):1297–1325. https://doi.org/10.1152/physrev.00041.2015
Beg MS, Brenner AJ, Sachdev J, Borad M, Kang Y-K, Stoudemire J, Smith S, Bader AG, Kim S, Hong DS (2017) Phase I study of MRX34, a liposomal miR-34a mimic, administered twice weekly in patients with advanced solid tumors. Invest New Drugs 35(2):180–188. https://doi.org/10.1007/s10637-016-0407-y
Bell JC, Jukam D, Teran NA, Risca VI, Smith OK, Johnson WL, Skotheim JM, Greenleaf WJ, Straight AF (2018) Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. Elife 7:e27024. https://doi.org/10.7554/eLife.27024
Benson MD, Waddington-Cruz M, Berk JL, Polydefkis M, Dyck PJ, Wang AK, Planté-Bordeneuve V, Barroso FA, Merlini G, Obici L, Scheinberg M, Brannagan TH, Litchy WJ, Whelan C, Drachman BM, Adams D, Heitner SB, Conceição I, Schmidt HH, Vita G (2018) Inotersen Treatment for Patients with Hereditary Transthyretin Amyloidosis. N Engl J Med 379(1):22–31. https://doi.org/10.1056/nejmoa1716793
Bernstein HD, Zopf D, Freymann DM, Walter P (1993) Functional substitution of the signal recognition particle 54-kDa subunit by its Escherichia coli homolog. Proc Natl Acad Sci USA 90(11):5229–5233. https://doi.org/10.1073/pnas.90.11.5229
Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36(Database issue):D149-153. https://doi.org/10.1093/nar/gkm995
Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S (2013) Quantitative transcriptomics using designed primer-based amplification. Sci Rep 3(1). https://doi.org/10.1038/srep01740
Bhattacharya A, Cui Y (2015) SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions. Nucleic Acids Res 44(D1):D1005–D1010. https://doi.org/10.1093/nar/gkv1220
Bhattacharya A, Ziebarth JD, Cui Y (2013) PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res 42(D1):D86–D91. https://doi.org/10.1093/nar/gkt1028
Bhattacharyya M, Das M, Bandyopadhyay S (2012) miRT: A Database of Validated Transcription Start Sites of Human MicroRNAs. Genomics Proteomics Bioinforma 10(5):310–316. https://doi.org/10.1016/j.gpb.2012.08.005
Bhatti GK, Khullar N, Sidhu IS, Navik US, Reddy AP, Reddy PH, Bhatti JS (2021) Emerging role of non-coding RNA in health and disease. Metab Brain Dis 36(6):1119–1134. https://doi.org/10.1007/s11011-021-00739-y
Bo X, Wang S (2004) TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatics 21(8):1401–1402. https://doi.org/10.1093/bioinformatics/bti211
Bonauer A, Carmona G, Iwasaki M, Mione M, Koyanagi M, Fischer A, Burchfield J, Fox H, Doebele C, Ohtani K, Chavakis E, Potente M, Tjwa M, Urbich C, Zeiher AM, Dimmeler S (2009) MicroRNA-92a Controls Angiogenesis and Functional Recovery of Ischemic Tissues in Mice. Science 324(5935):1710–1713. https://doi.org/10.1126/science.1174381
Bottini S, Hamouda-Tekaya N, Tanasa B, Zaragosi L-E, Grandjean V, Repetto E, Trabucchi M (2017) From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data. Nucleic Acids Res gkx007. https://doi.org/10.1093/nar/gkx007
Broadbent HM, Peden JF, Lorkowski S, Goel A, Ongen H, Green F, Clarke R, Collins R, Franzosi MG, Tognoni G, Seedorf U, Rust S, Eriksson P, Hamsten A, Farrall M, Watkins H (2007) Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet 17(6):806–814. https://doi.org/10.1093/hmg/ddm352
Bu D, Yu K, Sun S, Xie C, Skogerbo G, Miao R, Xiao H, Liao Q, Luo H, Zhao G, Zhao H, Liu Z, Liu C, Chen R, Zhao Y (2011) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40(D1):D210–D215. https://doi.org/10.1093/nar/gkr1175
Buske FA, Bauer DC, Mattick JS, Bailey TL (2012) Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res 22(7):1372–1381. https://doi.org/10.1101/gr.130237.111
Cacchiarelli D, Legnini I, Martone J, Cazzella V, D’Amico A, Bertini E, Bozzoni I (2011) miRNAs as serum biomarkers for Duchenne muscular dystrophy. EMBO Mol Med 3(5):258–265. https://doi.org/10.1002/emmm.201100133
Cai Y, Yang Y, Chen X, He D, Zhang X, Wen X, Hu J, Fu C, Qiu D, Jose PA, Zeng C, Zhou L (2016) Circulating “LncPPARδ” From Monocytes as a Novel Biomarker for Coronary Artery Diseases. Medicine 95(6):e2360. https://doi.org/10.1097/md.0000000000002360
Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, Wang S, Du Z, Hu N, Yu X, Chen J, Wang L, Yang X, He S, Xue Y (2020) RIC-seq for global in situ profiling of RNA–RNA spatial interactions. Nature 582(7812):432–437. https://doi.org/10.1038/s41586-020-2249-1
Cao Z, Pan X, Yang Y, Huang Y, Shen H-B (2018) The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinforma (Oxford England) 34(13):2185–2194. https://doi.org/10.1093/bioinformatics/bty085
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) (2005). The transcriptional landscape of the mammalian genome. Science 309(5740):1559–1563. https://doi.org/10.1126/science.1112014
Carrieri C, Forrest ARR, Santoro C, Persichetti F, Carninci P, Zucchelli S, and Gustincich S (2015) Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells’ differentiation in vitro and in neurochemical models of Parkinson’s disease. Front Cell Neurosci 9. https://doi.org/10.3389/fncel.2015.00114
Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136(4):642–655. https://doi.org/10.1016/j.cell.2009.01.035
Castrignano T, Canali A, Grillo G, Liuni S, Mignone F, Pesole G (2004) CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. Nucleic Acids Res 32(Web Server):W624–W627. https://doi.org/10.1093/nar/gkh486
Chandler RJ, Venditti CP (2019) Gene Therapy for Methylmalonic Acidemia: Past, Present, and Future. Hum Gene Ther 30(10):1236–1244. https://doi.org/10.1089/hum.2019.113
Chang K-H, Wu Y-R, Chen C-M (2017) Down-regulation of miR-9* in the peripheral leukocytes of Huntington’s disease patients. Orphanet J Rare Dis 12(1). https://doi.org/10.1186/s13023-017-0742-x
Chen C-J, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E (2012) ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 28(23):3147–3149. https://doi.org/10.1093/bioinformatics/bts587
Chen G, Huang S, Song F, Zhou Y, He X (2020) Lnc-Ang362 is a pro-fibrotic long non-coding RNA promoting cardiac fibrosis after myocardial infarction by suppressing Smad7. Arch Biochem Biophys 685:108354. https://doi.org/10.1016/j.abb.2020.108354
Chen J, Guo J, Cui X, Dai Y, Tang Z, Qu J, Raj JU, Hu Q, Gou D (2018) The Long Noncoding RNA LnRPT Is Regulated by PDGF-BB and Modulates the Proliferation of Pulmonary Artery Smooth Muscle Cells. Am J Respir Cell Mol Biol 58(2):181–193. https://doi.org/10.1165/rcmb.2017-0111OC
Chen J, Hu Q, Zhang B-F, Liu X-P, Yang S, Jiang H (2019) Long noncoding RNA UCA1 inhibits ischaemia/reperfusion injury induced cardiomyocytes apoptosis via suppression of endoplasmic reticulum stress. Genes Genomics 41(7):803–810. https://doi.org/10.1007/s13258-019-00806-w
Chen J-F, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang D-Z (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38(2):228–233. https://doi.org/10.1038/ng1725
Chen S, Chen R, Zhang T, Lin S, Chen Z, Zhao B, Li H, Wu S (2018) Relationship of cardiovascular disease risk factors and noncoding RNAs with hypertension: a case-control study. BMC Cardiovasc Disord 18(1):58. https://doi.org/10.1186/s12872-018-0795-3
Chen X, Han P, Zhou T, Guo X, Song X, Li Y (2016) circRNADb: a comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep 6(1). https://doi.org/10.1038/srep34985
Chen X, Sun Y-Z, Zhang D-H, Li J-Q, Yan G-Y, An J-Y, You Z-H (2017) NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations. Database 2017. https://doi.org/10.1093/database/bax057
Chen Y, Wu F, Chen Z, He Z, Wei Q, Zeng W, Chen K, Xiao F, Yuan Y, Weng X, Zhou Y, Zhou X (2020) Acrylonitrile-Mediated Nascent RNA Sequencing for Transcriptome-Wide Profiling of Cellular RNA Dynamics. Advanced Science 7(8):1900997. https://doi.org/10.1002/advs.201900997
Chénais B (2022) Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants. Int J Mol Sci 23(5):2551. https://doi.org/10.3390/ijms23052551
Cheng C, Spengler RM, Keiser MS, Monteys AM, Rieders JM, Ramachandran S, Davidson BL (2018) The long non-coding RNA NEAT1 is elevated in polyglutamine repeat expansion diseases and protects from disease gene-dependent toxicities. Hum Mol Genet 27(24):4303–4314. https://doi.org/10.1093/hmg/ddy331
Cheng J, Metge F, Dieterich C (2015) Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics 32(7):1094–1096. https://doi.org/10.1093/bioinformatics/btv656
Cheng P-H, Li C-L, Chang Y-F, Tsai S-J, Lai Y-Y, Chan AWS, Chen C-M, Yang S-H (2013) miR-196a Ameliorates Phenotypes of Huntington Disease in Cell, Transgenic Mouse, and Induced Pluripotent Stem Cell Models. Am J Human Genet 93(2):306–312. https://doi.org/10.1016/j.ajhg.2013.05.025
Cheng W-C, Chung I-F, Huang T-S, Chang S-T, Sun H-J, Tsai C-F, Liang M-L, Wong T-T, Wang H-W (2012) YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 41(D1):D285–D294. https://doi.org/10.1093/nar/gks1238
Cheng Y, Tan N, Yang J, Liu X, Cao X, He P, Dong X, Qin S, Zhang C (2010) A translational study of circulating cell-free microRNA-1 in acute myocardial infarction. Clin Sci 119(2):87–95. https://doi.org/10.1042/cs20090645
Chhabra R (2021) The journey of noncoding RNA from bench to clinic. Translational Biotechnology 165–201. https://doi.org/10.1016/b978-0-12-821972-0.00016-2
Chi KN, Eisenhauer E, Fazli L, Jones EC, Goldenberg SL, Powers J, Tu D, Gleave ME (2005) A phase I pharmacokinetic and pharmacodynamic study of OGX-011, a 2’-methoxyethyl antisense oligonucleotide to clusterin, in patients with localized prostate cancer. J Natl Cancer Inst 97(17):1287–1296. https://doi.org/10.1093/jnci/dji252
Chi KN, Yu EY, Jacobs C, Bazov J, Kollmannsberger C, Higano CS, Mukherjee SD, Gleave ME, Stewart PS, Hotte SJ (2016) A phase I dose-escalation study of apatorsen (OGX-427), an antisense inhibitor targeting heat shock protein 27 (Hsp27), in patients with castration-resistant prostate cancer and other advanced cancers. Ann Oncol 27(6):1116–1122. https://doi.org/10.1093/annonc/mdw068
Chi T, Lin J, Wang M, Zhao Y, Liao Z, Wei P (2021) Non-coding RNA as biomarkers for type 2 diabetes development and clinical management. Front Endocrinol 12. https://doi.org/10.3389/fendo.2021.630032
Cho HJ, Liu G, Jin SM, Parisiadou L, Xie C, Yu J, Sun L, Ma B, Ding J, Vancraenenbroeck R, Lobbestael E, Baekelandt V, Taymans J-M, He P, Troncoso JC, Shen Y, Cai H (2012) MicroRNA-205 regulates the expression of Parkinson’s disease-related leucine-rich repeat kinase 2 protein. Hum Mol Genet 22(3):608–620. https://doi.org/10.1093/hmg/dds470
Cho H, Kaelin WG (2016) Targeting HIF2 in Clear Cell Renal Cell Carcinoma. Cold Spring Harb Symp Quant Biol 81:113–121. https://doi.org/10.1101/sqb.2016.81.030833
Cho S, Jun Y, Lee S, Choi H-S, Jung S, Jang Y, Park C, Kim S, Lee S, Kim W (2011) miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 39(Database issue):D158-162. https://doi.org/10.1093/nar/gkq1094
Chou C-H, Lin F-M, Chou M-T, Hsu S-D, Chang T-H, Weng S-L, Shrestha S, Hsiao C-C, Hung J-H, Huang H-D (2013) A computational approach for identifying microRNA-target interactions using high throughput CLIP and PAR-CLIP sequencing. BMC Genomics 14(S1). https://doi.org/10.1186/1471-2164-14-s1-s2
Chou C-H, Shrestha S, Yang C-D, Chang N-W, Lin Y-L, Liao K-W, Huang W-C, Sun T-H, Tu S-J, Lee W-H, Chiew M-Y, Tai C-S, Wei T-Y, Tsai T-R, Huang H-T, Wang C-Y, Wu H-Y, Ho S-Y, Chen P-R, Chuang C-H (2018) miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res 46(D1):D296–D302. https://doi.org/10.1093/nar/gkx1067
Chuang T-J, Wu C-S, Chen C-Y, Hung L-Y, Chiang T-W, Yang M-Y (2015) NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res 44(3):e29–e29. https://doi.org/10.1093/nar/gkv1013
Chung I-F, Chang S-J, Chen C-Y, Liu S-H, Li C-Y, Chan C-H, Shih C-C, Cheng W-C (2016) YM500v3: a database for small RNA sequencing in human cancer research. Nucleic Acids Res 45(D1):D925–D931. https://doi.org/10.1093/nar/gkw1084
Clote P (2005) RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res 33(Web Server):W600–W604. https://doi.org/10.1093/nar/gki382
Cordero P, Lucks JB, Das R (2012) An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics 28(22):3006–3008. https://doi.org/10.1093/bioinformatics/bts554
Corsten MF, Dennert R, Jochems S, Kuznetsova T, Devaux Y, Hofstra L, Wagner DR, Staessen JA, Heymans S, Schroen B (2010) Circulating MicroRNA-208b and MicroRNA-499 Reflect Myocardial Damage in Cardiovascular Disease. Circ: Cardiovasc Genetics 3(6):499–506. https://doi.org/10.1161/circgenetics.110.957415
Cortes J, Kantarjian H, Ball ED, DiPersio J, Kolitz JE, Fernandez HF, Goodman M, Borthakur G, Baer MR, Wetzler M (2011) Phase 2 randomized study of p53 antisense oligonucleotide (cenersen) plus idarubicin with or without cytarabine in refractory and relapsed acute myeloid leukemia. Cancer 118(2):418–427. https://doi.org/10.1002/cncr.26292
Cushing L, Kuang PP, Qian J, Shao F, Wu J, Little F, Thannickal VJ, Cardoso WV, Lü J (2011) miR-29 is a major regulator of genes associated with pulmonary fibrosis. Am J Respir Cell Mol Biol 45(2):287–294. https://doi.org/10.1165/rcmb.2010-0323OC
D’Alessandra Y, Carena MC, Spazzafumo L, Martinelli F, Bassetti B, Devanna P, Rubino M, Marenzi G, Colombo GI, Achilli F, Maggiolini S, Capogrossi MC, Pompilio G (2013) Diagnostic Potential of Plasmatic MicroRNA Signatures in Stable and Unstable Angina. PLoS ONE 8(11):e80345. https://doi.org/10.1371/journal.pone.0080345
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(suppl_2):W155–W159. https://doi.org/10.1093/nar/gkr319
Das E, Jana NR, Bhattacharyya NP (2013) MicroRNA-124 targets CCNA2 and regulates cell cycle in STHdh(Q111)/Hdh(Q111) cells. Biochem Biophys Res Commun 437(2):217–224. https://doi.org/10.1016/j.bbrc.2013.06.041
Das E, Jana N, Bhattacharyya N (2015) Delayed Cell Cycle Progression in STHdhQ111/HdhQ111 Cells, a Cell Model for Huntington’s Disease Mediated by microRNA-19a, microRNA-146a and microRNA-432. MicroRNA 4(2):86–100. https://doi.org/10.2174/2211536604666150713105606
de Mena L, Coto E, Cardo LF, Díaz M, Blázquez M, Ribacoba R, Salvador C, Pastor P, Samaranch Ll, Moris G, Menéndez M, Corao AI, Alvarez V (2010) Analysis of theMicro-RNA-133andPITX3genes in Parkinson’s disease. Am J Med Genetics Part B: Neuropsychiatr Genetics 9999B:n/a-n/a. https://doi.org/10.1002/ajmg.b.31086
De Velasco MA, Kura Y, Sakai K, Hatanaka Y, Davies BR, Campbell H, Klein S, Kim Y, MacLeod AR, Sugimoto K, Yoshikawa K, Nishio K, Uemura H (2019) Targeting castration-resistant prostate cancer with androgen receptor antisense oligonucleotide therapy. JCI Insight 4(17):122688. https://doi.org/10.1172/jci.insight.122688
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789. https://doi.org/10.1101/gr.132159.111
Di Liddo A, de OliveiraFreitasMachado C, Fischer S, Ebersberger S, Heumüller AW, Weigand JE, Müller-McNicoll M, Zarnack K (2019) A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress. J Mol Cell Biol 11(10):829–844. https://doi.org/10.1093/jmcb/mjz094
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T (2012) Landscape of transcription in human cells. Nature 489(7414):101–108. https://doi.org/10.1038/nature11233
Dong R, Ma X-K, Li G-W, Yang L (2018) CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison. Genomics Proteomics Bioinforma 16(4):226–233. https://doi.org/10.1016/j.gpb.2018.08.001
Dong Y, Han L-L, Xu Z-X (2018) Suppressed microRNA-96 inhibits iNOS expression and dopaminergic neuron apoptosis through inactivating the MAPK signaling pathway by targeting CACNG5 in mice with Parkinson’s disease. Mol Med (Cambridge Mass) 24(1):61. https://doi.org/10.1186/s10020-018-0059-9
Du J, Yang S-T, Liu J, Zhang K-X, Leng J-Y (2019) Silence of LncRNA GAS5 Protects Cardiomyocytes H9c2 against Hypoxic Injury via Sponging miR-142–5p. Mol Cells 42(5):397–405. https://doi.org/10.14348/molcells.2018.0180
Eisenberg I, Eran A, Nishino I, Moggio M, Lamperti C, Amato AA, Lidov HG, Kang PB, North KN, Mitrani-Rosenbaum S, Flanigan KM, Neely LA, Whitney D, Beggs AH, Kohane IS, Kunkel LM (2007) Distinctive patterns of microRNA expression in primary muscular disorders. Proc Natl Acad Sci 104(43):17016–17021. https://doi.org/10.1073/pnas.0708115104
El Dika I, Lim HY, Yong WP, Lin C, Yoon J, Modiano M, Freilich B, Choi HJ, Chao T, Kelley RK, Brown J, Knox J, Ryoo B, Yau T, Abou-Alfa GK (2018) An Open-Label, Multicenter, Phase I, Dose Escalation Study with Phase II Expansion Cohort to Determine the Safety, Pharmacokinetics, and Preliminary Antitumor Activity of Intravenous TKM-080301 in Subjects with Advanced Hepatocellular Carcinoma. Oncologist 24(6):747. https://doi.org/10.1634/theoncologist.2018-0838
Espinoza S, Scarpato M, Damiani D, Managò F, Mereu M, Contestabile A, Peruzzo O, Carninci P, Santoro C, Papaleo F, Mingozzi F, Ronzitti G, Zucchelli S, Gustincich S (2020) SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson’s Disease. Mol Ther 28(2):642–652. https://doi.org/10.1016/j.ymthe.2019.08.005
Fabbri E, Borgatti M, Montagner G, Bianchi N, Finotti A, Lampronti I, Bezzerri V, Dechecchi MC, Cabrini G, Gambari R (2014) Expression of microRNA-93 and Interleukin-8 duringPseudomonas aeruginosa–Mediated Induction of Proinflammatory Responses. Am J Respir Cell Mol Biol 50(6):1144–1155. https://doi.org/10.1165/rcmb.2013-0160oc
Fabbri E, Tamanini A, Jakova T, Gasparello J, Manicardi A, Corradini R, Sabbioni G, Finotti A, Borgatti M, Lampronti I, Munari S, Dechecchi M, Cabrini G, Gambari R (2017) A Peptide Nucleic Acid against MicroRNA miR-145-5p Enhances the Expression of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) in Calu-3 Cells. Molecules 23(1):71. https://doi.org/10.3390/molecules23010071
Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y (2015) Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol 16(1). https://doi.org/10.1186/s13059-015-0706-1
Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S (2011) DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 39(suppl_2):W112–W117. https://doi.org/10.1093/nar/gkr357
Feng J, Sun G, Yan J, Noltner K, Li W, Buzin CH, Longmate J, Heston LL, Rossi J, Sommer SS (2009) Evidence for X-chromosomal schizophrenia associated with microRNA alterations. PLoS ONE 4(7):e6121. https://doi.org/10.1371/journal.pone.0006121
Feng L, Liao Y-T, He J-C, Xie C-L, Chen S-Y, Fan H-H, Su Z-P, Wang Z (2018) Plasma long noncoding RNA BACE1 as a novel biomarker for diagnosis of Alzheimer disease. BMC Neurol 18(1). https://doi.org/10.1186/s12883-017-1008-x
Fichtlscherer S, De Rosa S, Fox H, Schwietz T, Fischer A, Liebetrau C, Weber M, Hamm CW, Röxe T, Müller-Ardogan M, Bonauer A, Zeiher AM, Dimmeler S (2010) Circulating MicroRNAs in Patients With Coronary Artery Disease. Circ Res 107(5):677–684. https://doi.org/10.1161/circresaha.109.215566
Foessl I, Kotzbeck P, Obermayer-Pietsch B (2019) miRNAs as novel biomarkers for bone related diseases. J Lab Precis Med 4:2. https://doi.org/10.21037/jlpm.2018.12.06
Fragkouli A, Doxakis E (2014) miR-7 and miR-153 protect neurons against MPP+-induced cell death via upregulation of mTOR pathway. Front Cell Neurosci 8. https://doi.org/10.3389/fncel.2014.00182
Friedberg JW, Kim H, McCauley M, Hessel EM, Sims P, Fisher DC, Nadler LM, Coffman RL, Freedman AS (2005) Combination immunotherapy with a CpG oligonucleotide (1018 ISS) and rituximab in patients with non-Hodgkin lymphoma: increased interferon-α/β–inducible gene expression, without significant toxicity. Blood 105(2):489–495. https://doi.org/10.1182/blood-2004-06-2156
Fritegotto C, Ferrati C, Pegoraro V, Angelini C (2017) Micro-RNA expression in muscle and fiber morphometry in myotonic dystrophy type 1. Neurol Sci 38(4):619–625. https://doi.org/10.1007/s10072-017-2811-2
Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2019) MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res 48(D1):D132–D141. https://doi.org/10.1093/nar/gkz885
Fu L, Cao Y, Wu J, Peng Q, Nie Q, Xie X (2021) UFold: fast and accurate RNA secondary structure prediction with deep learning. Nucleic Acids Res 50(3):e14–e14. https://doi.org/10.1093/nar/gkab1074
Fu X-D (2014) Non-coding RNA: a new frontier in regulatory biology. Natl Sci Rev 1(2):190–204. https://doi.org/10.1093/nsr/nwu008
Fukunaga T, Iwakiri J, Ono Y, Hamada M (2019) LncRRI search: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data. Front Genet 10. https://doi.org/10.3389/fgene.2019.00462
Fukuoka M, Takahashi M, Fujita H, Chiyo T, Popiel HA, Watanabe S, Furuya H, Murata M, Wada K, Okada T, Nagai Y, Hohjoh H (2018) Supplemental Treatment for Huntington’s Disease with miR-132 that Is Deficient in Huntington’s Disease Brain. Mol Ther - Nucleic Acids 11:79–90. https://doi.org/10.1016/j.omtn.2018.01.007
Gagen M (2005) Inherent size constraints on prokaryote gene networks due to ?accelerating? growth. Theory Biosci 123(4):381–411. https://doi.org/10.1016/j.thbio.2005.02.002
Gagliardi S, Zucca S, Pandini C, Diamanti L, Bordoni M, Sproviero D, Arigoni M, Olivero M, Pansarasa O, Ceroni M, Calogero R, Cereda C (2018) Long non-coding and coding RNAs characterization in peripheral blood mononuclear cells and spinal cord from amyotrophic lateral sclerosis patients. Sci Rep 8(1). https://doi.org/10.1038/s41598-018-20679-5
Gamazon ER, Im H-K, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W (2010) ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets. PLoS ONE 5(10):e13534. https://doi.org/10.1371/journal.pone.0013534
Gambardella S, Rinaldi F, Lepore SM, Viola A, Loro E, Angelini C, Vergani L, Novelli G, Botta A (2010) Overexpression of microRNA-206 in the skeletal muscle from myotonic dystrophy type 1 patients. J Transl Med 8:48. https://doi.org/10.1186/1479-5876-8-48
Gao J-X, Li Y, Wang S-N, Chen X-C, Lin L-L, Zhang H (2018) Overexpression of microRNA-183 promotes apoptosis of substantia nigra neurons via the inhibition of OSMR in a mouse model of Parkinson’s disease. Int J Mol Med. https://doi.org/10.3892/ijmm.2018.3982
Gao L, Liu Y, Guo S, Yao R, Wu L, Xiao L, Wang Z, Liu Y, Zhang Y (2017) Circulating Long Noncoding RNA HOTAIR is an Essential Mediator of Acute Myocardial Infarction. Cell Physiol Biochem 44(4):1497–1508. https://doi.org/10.1159/000485588
Gao Y, Wang J, Zhao F (2015) CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol 16(1). https://doi.org/10.1186/s13059-014-0571-3
Gao Y, Wang P, Wang Y, Ma X, Zhi H, Zhou D, Li X, Fang Y, Shen W, Xu Y, Shang S, Wang L, Wang L, Ning S, Li X (2018) Lnc2Cancer v20: updated database of experimentally supported long non-coding RNAs in human cancers. Nucleic Acids Res 47(D1):D1028–D1033. https://doi.org/10.1093/nar/gky1096
Gardini A (2017) Global Run-On sequencing (GRO-seq). Methods Mol Biol (Clifton N.J.) 1468:111–120. https://doi.org/10.1007/978-1-4939-4035-6_9
Gasparello J, Fabbri E, Bianchi N, Breveglieri G, Zuccato C, Borgatti M, Gambari R, Finotti A (2017) BCL11A mRNA Targeting by miR-210: A Possible Network Regulating γ-Globin Gene Expression. Int J Mol Sci 18(12):2530. https://doi.org/10.3390/ijms18122530
Gaughwin PM, Ciesla M, Lahiri N, Tabrizi SJ, Brundin P, Björkqvist M (2011) Hsa-miR-34b is a plasma-stable microRNA that is elevated in pre-manifest Huntington’s disease. Hum Mol Genet 20(11):2225–2237. https://doi.org/10.1093/hmg/ddr111
Gautheret D, Lambert A (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles 1 1Edited by J. Doudna. J Mol Biol 313(5):1003–1011. https://doi.org/10.1006/jmbi.2001.5102
Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG (2014) microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nature. Communications 5(1). https://doi.org/10.1038/ncomms6700
Ghafouri-Fard S, Poulet C, Malaise M, Abak A, Mahmud Hussen B, Taheriazam A, … Hallajnejad M (2021) The Emerging Role of Non-Coding RNAs in Osteoarthritis. Front Immunol 12. https://doi.org/10.3389/fimmu.2021.773171
Ghosal S, Das S, Sen R, Basak P, Chakrabarti J (2013) Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet 4. https://doi.org/10.3389/fgene.2013.00283
Ghose J, Sinha M, Das E, Jana NR, Bhattacharyya NP (2011) Regulation of miR-146a by RelA/NFkB and p53 in STHdh(Q111)/Hdh(Q111) cells, a cell model of Huntington’s disease. PLoS ONE 6(8):e23837. https://doi.org/10.1371/journal.pone.0023837
Gidlöf O, Smith JG, Miyazu K, Gilje P, Spencer A, Blomquist S, Erlinge D (2013) Circulating cardioenriched microRNAs are associated with long-term prognosis following myocardial infarction. BMC Cardiovasc Disord 13(1). https://doi.org/10.1186/1471-2261-13-12
Gillen AE, Gosalia N, Leir S-H, Harris A (2011) microRNA regulation of expression of the cystic fibrosis transmembrane conductance regulator gene. Biochem J 438(1):25–32. https://doi.org/10.1042/bj20110672
Giordani L, Sandoná M, Rotini A, Puri P, Consalvi S, Saccone V (2014) Muscle-specific microRNAs as biomarkers of Duchenne Muscular Dystrophy progression and response to therapies. Rare Dis 2(1):e974969. https://doi.org/10.4161/21675511.2014.974969
Glažar P, Papavasileiou P, Rajewsky N (2014) circBase: a database for circular RNAs. RNA 20(11):1666–1670. https://doi.org/10.1261/rna.043687.113
Golan T, Khvalevsky EZ, Hubert A, Gabai RM, Hen N, Segal A, Domb A, Harari G, David EB, Raskin S, Goldes Y, Goldin E, Eliakim R, Lahav M, Kopleman Y, Dancour A, Shemi A, Galun E (2015) RNAi therapy targeting KRAS in combination with chemotherapy for locally advanced pancreatic cancer patients. Oncotarget 6(27):24560–24570. https://doi.org/10.18632/oncotarget.4183
Gomez IG, MacKenna DA, Johnson BG, Kaimal V, Roach AM, Ren S, Nakagawa N, Xin C, Newitt R, Pandya S, Xia T-H, Liu X, Borza D-B, Grafals M, Shankland SJ, Himmelfarb J, Portilla D, Liu S, Chau BN, Duffield JS (2014) Anti–microRNA-21 oligonucleotides prevent Alport nephropathy progression by stimulating metabolic pathways. J Clin Investig 125(1):141–156. https://doi.org/10.1172/jci75852
Gong J, Liu C, Liu W, Xiang Y, Diao L, Guo A-Y, Han L (2017) LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleic Acids Res 45(D1):D79–D84. https://doi.org/10.1093/nar/gkw835
Gong J, Shao D, Xu K, Lu Z, JohnLu Z, Yang YT, Zhang QC (2017) RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res 46(D1):D194–D201. https://doi.org/10.1093/nar/gkx864
Gragoudas ES, Adamis AP, Cunningham ET, Feinsod M, Guyer DR (2004) Pegaptanib for Neovascular Age-Related Macular Degeneration. N Engl J Med 351(27):2805–2816. https://doi.org/10.1056/nejmoa042760
Greco S, De Simone M, Colussi C, Zaccagnini G, Fasanaro P, Pescatori M, Cardani R, Perbellini R, Isaia E, Sale P, Meola G, Capogrossi MC, Gaetano C, Martelli F (2009) Common micro-RNA signature in skeletal muscle damage and regeneration induced by Duchenne muscular dystrophy and acute ischemia. FASEB J 23(10):3335–3346. https://doi.org/10.1096/fj.08-128579
Greco S, Zaccagnini G, Fuschi P, Voellenkle C, Carrara M, Sadeghi I, Bearzi C, Maimone B, Castelvecchio S, Stellos K, Gaetano C, Menicanti L, Martelli F (2017) Increased BACE1-AS long noncoding RNA and β-amyloid levels in heart failure. Cardiovasc Res 113(5):453–463. https://doi.org/10.1093/cvr/cvx013
Greco S, Zaccagnini G, Perfetti A, Fuschi P, Valaperta R, Voellenkle C, Castelvecchio S, Gaetano C, Finato N, Beltrami AP, Menicanti L, Martelli F (2016) Long noncoding RNA dysregulation in ischemic heart failure. J Transl Med 14(1):183. https://doi.org/10.1186/s12967-016-0926-5
Griffiths-Jones S (2003) Rfam: an RNA family database. Nucleic Acids Res 31(1):439–441. https://doi.org/10.1093/nar/gkg006
Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA Websuite. Nucleic Acids Res 36(Web Server):W70–W74. https://doi.org/10.1093/nar/gkn188
Guibinga G-H (2015) MicroRNAs: tools of mechanistic insights and biological therapeutics discovery for the rare neurogenetic syndrome Lesch-Nyhan disease (LND). Adv Genet 90:103–131. https://doi.org/10.1016/bs.adgen.2015.06.001
Guo JU, Agarwal V, Guo H, Bartel DP (2014) Expanded identification and characterization of mammalian circular RNAs. Genome Biol 15(7). https://doi.org/10.1186/s13059-014-0409-z
Guo J-C, Fang S-S, Wu Y, Zhang J-H, Chen Y, Liu J, Wu B, Wu J-R, Li E-M, Xu L-Y, Sun L, Zhao Y (2019) CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition. Nucleic Acids Res 47(W1):W516–W522. https://doi.org/10.1093/nar/gkz400
Guo Z-W, Xie C, Li K, Zhai X-M, Cai G-X, Yang X-X, and Wu Y-S (2019b) SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers. Database 2019b. https://doi.org/10.1093/database/baz027
Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482(7385):339–346. https://doi.org/10.1038/nature10887
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364):295–300. https://doi.org/10.1038/nature10398
Habtemariam BA, Karsten V, Attarwala H, Goel V, Melch M, Clausen VA, Garg P, Vaishnaw AK, Sweetser MT, Robbie GJ, Vest J (2020) Single-Dose Pharmacokinetics and Pharmacodynamics of Transthyretin Targeting N-acetylgalactosamine–Small Interfering Ribonucleic Acid Conjugate, Vutrisiran Healthy Subjects. Clin Pharmacol Ther 109(2):372–382. https://doi.org/10.1002/cpt.1974
Hackenberg M, Rodriguez-Ezpeleta N, Aransay AM (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 39(suppl):W132–W138. https://doi.org/10.1093/nar/gkr247
Hagemann-Jensen M, Abdullayev I, Sandberg R, Faridani OR (2018) Small-seq for single-cell small-RNA sequencing. Nat Protoc 13(10):2407–2424. https://doi.org/10.1038/s41596-018-0049-y
Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs. PLoS Genet 9(6):e1003569. https://doi.org/10.1371/journal.pgen.1003569
Hansen TB, Venø MT, Kjems J, Damgaard CK (2014) miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs. Nucleic Acids Res 42(16):e124. https://doi.org/10.1093/nar/gku598
Harafuji N, Schneiderat P, Walter MC, Chen Y-W (2013) miR-411 is up-regulated in FSHD myoblasts and suppresses myogenic factors. Orphanet J Rare Dis 8(1):55. https://doi.org/10.1186/1750-1172-8-55
Hassan F, Nuovo GJ, Crawford M, Boyaka PN, Kirkby S, Nana-Sinkam SP, Cormet-Boyaka E (2012) MiR-101 and miR-144 regulate the expression of the CFTR chloride channel in the lung. PLoS ONE 7(11):e50837. https://doi.org/10.1371/journal.pone.0050837
Haunsberger SJ, Connolly NMC, Prehn JHM (2016) miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions. Bioinformatics btw660. https://doi.org/10.1093/bioinformatics/btw660
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M (2009) MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res 37(Web Server):W266–W272. https://doi.org/10.1093/nar/gkp412
Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I (2018) Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs. Nat Commun 9. https://doi.org/10.1038/s41467-018-02866-0
Heikkinen L, Kolehmainen M, Wong G (2011) Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map. Bioinformatics 27(9):1247–1254. https://doi.org/10.1093/bioinformatics/btr144
Hennessy EJ, van Solingen C, Scacalossi KR, Ouimet M, Afonso MS, Prins J, Koelwyn GJ, Sharma M, Ramkhelawon B, Carpenter S, Busch A, Chernogubova E, Matic LP, Hedin U, Maegdefessel L, Caffrey BE, Hussein MA, Ricci EP, Temel RE, Garabedian MJ (2018) The long noncoding RNA CHROME regulates cholesterol homeostasis in primates. Nat Metab 1(1):98–110. https://doi.org/10.1038/s42255-018-0004-9
Her L-S, Mao S-H, Chang C-Y, Cheng P-H, Chang Y-F, Yang H-I, Chen C-M, Yang S-H (2017) miR-196a Enhances Neuronal Morphology through Suppressing RANBP10 to Provide Neuroprotection in Huntington’s Disease. Theranostics 7(9):2452–2462. https://doi.org/10.7150/thno.18813
Hervé M, Ibrahim EC (2016) MicroRNA screening identifies a link between NOVA1 expression and a low level of IKAP in familial dysautonomia. Dis Model Mech 9(8):899–909. https://doi.org/10.1242/dmm.025841
Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL (2017) Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods 14(12):1198–1204. https://doi.org/10.1038/nmeth.4435
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J (2009) Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput Biol 5(9):e1000502. https://doi.org/10.1371/journal.pcbi.1000502
Holmes AP, Kirchhof P (2016) Pitx2 adjacent noncoding RNA. Circ Arrhythm Electrophysiol 9(1). https://doi.org/10.1161/circep.115.003808
Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen J-F, Akbarian S, Weng Z, Vonsattel JP, Myers RH (2015) miR-10b-5p expression in Huntington’s disease brain relates to age of onset and the extent of striatal involvement. BMC Med Genet 8(1). https://doi.org/10.1186/s12920-015-0083-3
Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M (2008) A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster. Mol Cell 32(5):685–695. https://doi.org/10.1016/j.molcel.2008.09.027
Hu J, Kong M, Ye Y, Hong S, Cheng L, Jiang L (2014) Serum miR-206 and other muscle-specific microRNAs as non-invasive biomarkers for Duchenne muscular dystrophy. J Neurochem 129(5):877–883. https://doi.org/10.1111/jnc.12662
Hu Y-W, Guo F-X, Xu Y-J, Li P, Lu Z-F, McVey DG, Zheng L, Wang Q, Ye JH, Kang C-M, Wu S-G, Zhao J-J, Ma X, Yang Z, Fang F-C, Qiu Y-R, Xu B-M, Xiao L, Wu Q, Wu L-M (2019) Long noncoding RNA NEXN-AS1 mitigates atherosclerosis by regulating the actin-binding protein NEXN. J Clin Investig 129(3):1115–1128. https://doi.org/10.1172/JCI98230
Huang GT, Athanassiou C, Benos PV (2011) mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res 39(suppl):W416–W423. https://doi.org/10.1093/nar/gkr276
Huang JC, Morris QD, Frey BJ (2007) Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. J Comput Biol 14(5):550–563. https://doi.org/10.1089/cmb.2007.r002
Huang S, Tao W, Guo Z, Cao J, Huang X (2019) Suppression of long noncoding RNA TTTY15 attenuates hypoxia-induced cardiomyocytes injury by targeting miR-455-5p. Gene 701:1–8. https://doi.org/10.1016/j.gene.2019.02.098
Huang Z, Shi J, Gao Y, Cui C, Zhang S, Li J, Zhou Y, Cui Q (2019) HMDD v3.0: a database for experimentally supported human microRNA–disease associations. Nucleic Acids Res 47(D1):D1013–D1017. https://doi.org/10.1093/nar/gky1010
Id Said B, Malkin D (2015) A functional variant in miR-605 modifies the age of onset in Li-Fraumeni syndrome. Cancer Genet 208(1–2):47–51. https://doi.org/10.1016/j.cancergen.2014.12.003
Imamachi N, Tani H, Mizutani R, Imamura K, Irie T, Suzuki Y, Akimitsu N (2014) BRIC-seq: A genome-wide approach for determining RNA stability in mammalian cells. Methods 67(1):55–63. https://doi.org/10.1016/j.ymeth.2013.07.014
Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol, 138–148. https://pubmed.ncbi.nlm.nih.gov/10786296/
Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y, Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 51(12):1087–1099. https://doi.org/10.1007/s10038-006-0070-9
Jaguszewski M, Osipova J, Ghadri J-R, Napp LC, Widera C, Franke J, Fijalkowski M, Nowak R, Fijalkowska M, Volkmann I, Katus HA, Wollert KC, Bauersachs J, Erne P, Luscher TF, Thum T, Templin C (2013) A signature of circulating microRNAs differentiates takotsubo cardiomyopathy from acute myocardial infarction. Eur Heart J 35(15):999–1006. https://doi.org/10.1093/eurheartj/eht392
Jakob P, Kacprowski T, Briand-Schumacher S, Heg D, Klingenberg R, Stähli BE, Jaguszewski M, Rodondi N, Nanchen D, Räber L, Vogt P, Mach F, Windecker S, Völker U, Matter CM, Lüscher TF, Landmesser U (2016) Profiling and validation of circulating microRNAs for cardiovascular events in patients presenting with ST-segment elevation myocardial infarction. Eur Heart J ehw563. https://doi.org/10.1093/eurheartj/ehw563
Janssen HLA, Reesink HW, Lawitz EJ, Zeuzem S, Rodriguez-Torres M, Patel K, van der Meer AJ, Patick AK, Chen A, Zhou Y, Persson R, King BD, Kauppinen S, Levin AA, Hodges MR (2013) Treatment of HCV Infection by Targeting MicroRNA. N Engl J Med 368(18):1685–1694. https://doi.org/10.1056/nejmoa1209026
Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32(5):453–461. https://doi.org/10.1038/nbt.2890
Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE (2012) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19(2):141–157. https://doi.org/10.1261/rna.035667.112
Jha A, Shankar R (2013) miReader: Discovering Novel miRNAs in Species without Sequenced Genome. PLoS ONE 8(6):e66857. https://doi.org/10.1371/journal.pone.0066857
Jiang Q, Ma R, Wang J, Wu X, Jin S, Peng J, Tan R, Zhang T, Li Y, Wang Y (2015) LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics 16(S3). https://doi.org/10.1186/1471-2164-16-s3-s2
Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37(Database):D98–D104. https://doi.org/10.1093/nar/gkn714
Jin L, Lin X, Yang L, Fan X, Wang W, Li S, Li J, Liu X, Bao M, Cui X, Yang J, Cui Q, Geng B, Cai J (2018) AK098656, a Novel Vascular Smooth Muscle Cell-Dominant Long Noncoding RNA Promotes Hypertension. Hypertension 71(2):262–272. https://doi.org/10.1161/hypertensionaha.117.09651
Johnson R (2012) Long non-coding RNAs in Huntington’s disease neurodegeneration. Neurobiol Dis 46(2):245–254. https://doi.org/10.1016/j.nbd.2011.12.006
Johnson R, Richter N, Jauch R, Gaughwin PM, Zuccato C, Cattaneo E, Stanton LW (2010) Human accelerated region 1 noncoding RNA is repressed by REST in Huntington’s disease. Physiol Genomics 41(3):269–274. https://doi.org/10.1152/physiolgenomics.00019.2010
Johnson R, Teh CH-L, Jia H, Vanisri RR, Pandey T, Lu Z-H, Buckley NJ, Stanton LW, Lipovich L (2008) Regulation of neural macroRNAs by the transcriptional repressor REST. RNA 15(1):85–96. https://doi.org/10.1261/rna.1127009
Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, Pardo-Manuel de Villena F, Baric RS, Heise MT, Peng X, Katze MG (2014) Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. RNA Biol 11(7):875–890. https://doi.org/10.4161/rna.29442
Joyce GF (1989) RNA evolution and the origins of life. Nature 338(6212):217–224. https://doi.org/10.1038/338217a0
Kabaria S, Choi DC, Chaudhuri AD, Mouradian MM, Junn E (2015) Inhibition of miR-34b and miR-34c enhances α-synuclein expression in Parkinson’s disease. FEBS Lett 589(3):319–325. https://doi.org/10.1016/j.febslet.2014.12.014
Kadri S, Hinman V, Benos PV (2009) HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinform 10(S1). https://doi.org/10.1186/1471-2105-10-s1-s35
Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY (2017) Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. Elife 6:e29224. https://doi.org/10.7554/eLife.29224
Kang J, Tang Q, He J, Li L, Yang N, Yu S, Wang M, Zhang Y, Lin J, Cui T, Hu Y, Tan P, Cheng J, Zheng H, Wang D, Su X, Chen W, Huang Y (2022) RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. Nucleic Acids Res 50(D1):D326–D332. https://doi.org/10.1093/nar/gkab997
Karagkouni D, Paraskevopoulou MD, Chatzopoulos S, Vlachos IS, Tastsoglou S, Kanellos I, Papadimitriou D, Kavakiotis I, Maniou S, Skoufos G, Vergoulis T, Dalamagas T, Hatzigeorgiou AG (2018) DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions. Nucleic Acids Res 46(D1):D239–D245. https://doi.org/10.1093/nar/gkx1141
Ke S, Yang Z, Yang F, Wang X, Tan J, Liao B (2019) Long Noncoding RNA NEAT1 Aggravates Aβ-Induced Neuronal Damage by Targeting miR-107 in Alzheimer’s Disease. Yonsei Med J 60(7):640–650. https://doi.org/10.3349/ymj.2019.60.7.640
Ke Z-P, Xu Y-J, Wang Z-S, Sun J (2019) RNA sequencing profiling reveals key mRNAs and long noncoding RNAs in atrial fibrillation. J Cell Biochem. https://doi.org/10.1002/jcb.29504
Keerthikumar S, Chisanga D, Ariyaratne D, Al Saffar H, Anand S, Zhao K, Samuel M, Pathan M, Jois M, Chilamkurti N, Gangoda L, Mathivanan S (2016) ExoCarta: A Web-Based Compendium of Exosomal Cargo. J Mol Biol 428(4):688–692. https://doi.org/10.1016/j.jmb.2015.09.019
Kent WJ (2002) BLAT–-The BLAST-Like Alignment Tool. Genome Res 12(4):656–664. https://doi.org/10.1101/gr.229202
Kim J, Fiesel FC, Belmonte KC, Hudec R, Wang W-X, Kim C, Nelson PT, Springer W, Kim J (2016) miR-27a and miR-27b regulate autophagic clearance of damaged mitochondria by targeting PTEN-induced putative kinase 1 (PINK1). Mol Neurodegener 11(1). https://doi.org/10.1186/s13024-016-0121-4
Kim J, Hu C, Moufawad El Achkar C, Black LE, Douville J, Larson A, Pendergast MK, Goldkind SF, Lee EA, Kuniholm A, Soucy A, Vaze J, Belur NR, Fredriksen K, Stojkovska I, Tsytsykova A, Armant M, DiDonato RL, Choi J, Cornelissen L (2019) Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. N Engl J Med 381(17):1644–1652. https://doi.org/10.1056/nejmoa1813279
Kim J-D, Lee A, Choi J, Park Y, Kang H, Chang W, Lee M-S, Kim J (2015) Epigenetic modulation as a therapeutic approach for pulmonary arterial hypertension. Exp Mol Med 47:e175. https://doi.org/10.1038/emm.2015.45
Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10(2):126–139. https://doi.org/10.1038/nrm2632
Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM (2018) Functional classification of long non-coding RNAs by k-mer content. Nat Genet 50(10):1474–1482. https://doi.org/10.1038/s41588-018-0207-8
Knudsen B, Hein J (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15(6):446–454. https://doi.org/10.1093/bioinformatics/15.6.446
Kocerha J, Xu Y, Prucha MS, Zhao D, Chan AW (2014) microRNA-128a dysregulation in transgenic Huntington’s disease monkeys. Molecular. Brain 7(1). https://doi.org/10.1186/1756-6606-7-46
Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, Gao G (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35(Web Server issue):W345-349. https://doi.org/10.1093/nar/gkm391
Kozomara A, Birgaoanu M, Griffiths-Jones S (2018) miRBase: from microRNA sequences to function. Nucleic Acids Res 47(D1):D155–D162. https://doi.org/10.1093/nar/gky1141
Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005) Combinatorial microRNA target predictions. Nat Genet 37(5):495–500. https://doi.org/10.1038/ng1536
Kremsner PG, Ahuad Guerrero RA, Arana-Arri E, Aroca Martinez GJ, Bonten M, Chandler R, Corral G, De Block EJL, Ecker L, Gabor JJ, Garcia Lopez CA, Gonzales L, Granados González MA, Gorini N, Grobusch MP, Hrabar AD, Junker H, Kimura A, Lanata CF, Lehmann C (2022) Efficacy and safety of the CVnCoV SARS-CoV-2 mRNA vaccine candidate in ten countries in Europe and Latin America (HERALD): a randomised, observer-blinded, placebo-controlled, phase 2b/3 trial. Lancet Infect Dis 22(3):329–340. https://doi.org/10.1016/s1473-3099(21)00677-0
Kruger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34(Web Server):W451–W454. https://doi.org/10.1093/nar/gkl243
Kudla G, Granneman S, Hahn D, Beggs JD, Tollervey D (2011) Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci USA 108(24):10010–10015. https://doi.org/10.1073/pnas.1017386108
Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang L-S, Leung YY (2019) DASHR 20: integrated database of human small non-coding RNA genes and mature products. Bioinforma (Oxford England) 35(6):1033–1039. https://doi.org/10.1093/bioinformatics/bty709
Kumarswamy R, Bauters C, Volkmann I, Maury F, Fetisch J, Holzmann A, Lemesle G, de Groote P, Pinet F, Thum T (2014) Circulating Long Noncoding RNA, LIPCAR, Predicts Survival in Patients With Heart Failure. Circ Res 114(10):1569–1575. https://doi.org/10.1161/circresaha.114.303915
Kung JTY, Colognori D, Lee JT (2013) Long Noncoding RNAs: Past, Present, and Future. Genetics 193(3):651–669. https://doi.org/10.1534/genetics.112.146704
Kunkanjanawan T, Carter RL, Prucha MS, Yang J, Parnpai R, Chan AWS (2016) miR-196a Ameliorates Cytotoxicity and Cellular Phenotype in Transgenic Huntington’s Disease Monkey Neural Cells. PLoS ONE 11(9):e0162788. https://doi.org/10.1371/journal.pone.0162788
Laganà A, Paone A, Veneziano D, Cascione L, Gasparini P, Carasi S, Russo F, Nigita G, Macca V, Giugno R, Pulvirenti A, Shasha D, Ferro A, Croce CM (2012) miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinformatics 28(23):3166–3168. https://doi.org/10.1093/bioinformatics/bts589
Lamb YN (2021) Inclisiran: First Approval. Drugs 81(3):389–395. https://doi.org/10.1007/s40265-021-01473-6
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller R-U (2007) A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell 129(7):1401–1414. https://doi.org/10.1016/j.cell.2007.04.040
Laskin JJ, Nicholas G, Lee C, Gitlitz B, Vincent M, Cormier Y, Stephenson J, Ung Y, Sanborn R, Pressnail B, Nugent F, Nemunaitis J, Gleave ME, Murray N, Hao D (2012) Phase I/II trial of custirsen (OGX-011), an inhibitor of clusterin, in combination with a gemcitabine and platinum regimen in patients with previously untreated advanced non-small cell lung cancer. J Thorac Oncol 7(3):579–586. https://doi.org/10.1097/JTO.0b013e31823f459c
Lee EC, Valencia T, Allerson C, Schairer A, Flaten A, Yheskel M, Kersjes K, Li J, Gatto S, Takhar M, Lockton S, Pavlicek A, Kim M, Chu T, Soriano R, Davis S, Androsavich JR, Sarwary S, Owen T, Kaplan J (2019) Discovery and preclinical evaluation of anti-miR-17 oligonucleotide RGLS4326 for the treatment of polycystic kidney disease. Nat Commun 10(1):4148. https://doi.org/10.1038/s41467-019-11918-y
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 10(3):442–458. https://doi.org/10.1038/nprot.2014.191
Lee TB, Yang K, Ko HJ, Shim JR, Choi BH, Lee JH, Ryu JH (2021) Successful defibrotide treatment of a patient with veno-occlusive disease after living-donor liver transplantation: A case report. Medicine 100(25):e26463. https://doi.org/10.1097/MD.0000000000026463
Leecharoenkiat K, Tanaka Y, Harada Y, Chaichompoo P, Sarakul O, Abe Y, Smith DR, Fucharoen S, Svasti S, Umemura T (2017) Plasma microRNA-451 as a novel hemolytic marker for β0-thalassemia/HbE disease. Mol Med Rep 15(5):2495–2502. https://doi.org/10.3892/mmr.2017.6326
Leung A, Trac C, Jin W, Lanting L, Akbany A, Sætrom P, Schones DE, Natarajan R (2013) Novel long noncoding RNAs are regulated by angiotensin II in vascular smooth muscle cells. Circ Res 113(3):266–278. https://doi.org/10.1161/CIRCRESAHA.112.300849
Leung YY, Ryvkin P, Ungar LH, Gregory BD, Wang L-S (2013) CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res 41(14):e137–e137. https://doi.org/10.1093/nar/gkt426
Li C, Brant E, Budak H, Zhang B (2021) CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement. J Zhejiang Univ Sci B 22(4):253–284. https://doi.org/10.1631/jzus.B2100009
Li C, Ni Y-Q, Xu H, Xiang Q-Y, Zhao Y, Zhan J-K, He J-Y, Li S, Liu Y-S (2021) Roles and mechanisms of exosomal non-coding RNAs in human health and diseases. Signal transduction and targeted. Therapy 6(1). https://doi.org/10.1038/s41392-021-00779-x
Li H, Liu X, Zhang L, Li X (2017) LncRNA BANCR facilitates vascular smooth muscle cell proliferation and migration through JNK pathway. Oncotarget 8(70):114568–114575. https://doi.org/10.18632/oncotarget.21603
Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X (2020) Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther 5(1):1–23. https://doi.org/10.1038/s41392-019-0089-y
Li H, Zheng L, Jiang A, Mo Y, Gong Q (2018) Identification of the biological affection of long noncoding RNA BC200 in Alzheimer’s disease. NeuroReport 29(13):1061–1067. https://doi.org/10.1097/WNR.0000000000001057
Li J, Han L, Roebuck P, Diao L, Liu L, Yuan Y, Weinstein JN, Liang H (2015) TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer. Can Res 75(18):3728–3737. https://doi.org/10.1158/0008-5472.CAN-15-0273
Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H (2014) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 42(D1):D92–D97. https://doi.org/10.1093/nar/gkt1248
Li X, Yang L, Chen L-L (2018) The Biogenesis, Functions, and Challenges of Circular RNAs. Mol Cell 71(3):428–442. https://doi.org/10.1016/j.molcel.2018.06.034
Li X, Zhou B, Chen L, Gou L-T, Li H, Fu X-D (2017) GRID-seq reveals the global RNA–chromatin interactome. Nat Biotechnol 35(10):940–950. https://doi.org/10.1038/nbt.3968
Li Z, Wang X, Wang W, Du J, Wei J, Zhang Y, Wang J, Hou Y (2017) Altered long non-coding RNA expression profile in rabbit atria with atrial fibrillation: TCONS_00075467 modulates atrial electrical remodeling by sponging miR-328 to regulate CACNA1C. J Mol Cell Cardiol 108:73–85. https://doi.org/10.1016/j.yjmcc.2017.05.009
Liang J, Wen J, Huang Z, Chen X, Zhang B, Chu L (2019) Small nucleolar RNAs: insight into their function in Cancer. Front Oncol 9. https://doi.org/10.3389/fonc.2019.00587
Liebow A, Li X, Racie T, Hettinger J, Bettencourt BR, Najafian N, Haslett P, Fitzgerald K, Holmes RP, Erbe D, Querbes W, Knight J (2016) An Investigational RNAi Therapeutic Targeting Glycolate Oxidase Reduces Oxalate Production in Models of Primary Hyperoxaluria. J Am Soc Nephrol 28(2):494–503. https://doi.org/10.1681/asn.2016030338
Lim LP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17(8):991–1008. https://doi.org/10.1101/gad.1074403
Lin N, Chang K-Y, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang C-S, Cunningham TJ, Head SR, Duester G, Dong PDS, Rana TM (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 53(6):1005–1019. https://doi.org/10.1016/j.molcel.2014.01.021
Lin Q, Hou S, Dai Y, Jiang N, Lin Y (2019) LncRNA HOTAIR targets miR-126-5p to promote the progression of Parkinson’s disease through RAB3IP. Biol Chem 400(9):1217–1228. https://doi.org/10.1515/hsz-2018-0431
Lindgreen S, Gardner PP, Krogh A (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinforma (Oxford England) 23(24):3304–3311. https://doi.org/10.1093/bioinformatics/btm525
Ling T-Y, Wang X-L, Chai Q, Lau T-W, Koestler CM, Park SJ, Daly RC, Greason KL, Jen J, Wu L-Q, Shen W-F, Shen W-K, Cha Y-M, Lee H-C (2013) Regulation of the SK3 channel by microRNA-499–potential role in atrial fibrillation. Heart Rhythm 10(7):1001–1009. https://doi.org/10.1016/j.hrthm.2013.03.005
Liu J, Gough J, Rost B (2006) Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines. PLoS Genet 2(4):e29. https://doi.org/10.1371/journal.pgen.0020029
Liu J, Li Y, Lin B, Sheng Y, Yang L (2017) HBL1 Is a Human Long Noncoding RNA that Modulates Cardiomyocyte Development from Pluripotent Stem Cells by Counteracting MIR1. Dev Cell 42(4):333-348.e5. https://doi.org/10.1016/j.devcel.2017.07.023
Liu L, Li Z, Liu C, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z, Ma L (2021) LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Res 50(D1):D190–D195. https://doi.org/10.1093/nar/gkab998
Liu Q, Wang J, Zhao Y, Li C-I, Stengel KR, Acharya P, Johnston G, Hiebert SW, Shyr Y (2017) Identification of active miRNA promoters from nuclear run-on RNA sequencing. Nucleic Acids Res 45(13):e121. https://doi.org/10.1093/nar/gkx318
Liu T, Zhang Q, Zhang J, Li C, Miao Y-R, Lei Q, Li Q, Guo A-Y (2019) EVmiRNA: a database of miRNA profiling in extracellular vesicles. Nucleic Acids Res 47(D1):D89–D93. https://doi.org/10.1093/nar/gky985
Liu X, Fan Z, Zhao T, Cao W, Zhang L, Li H, Xie Q, Tian Y, Wang B (2015) Plasma miR-1, miR-208, miR-499 as potential predictive biomarkers for acute myocardial infarction: An independent study of Han population. Exp Gerontol 72:230–238. https://doi.org/10.1016/j.exger.2015.10.011. Accessed 7 Oct 2015
Liu X, Wang S, Meng F, Wang J, Zhang Y, Dai E, Yu X, Li X, Jiang W (2012) SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expression. Bioinformatics 29(3):409–411. https://doi.org/10.1093/bioinformatics/bts698
Liu Y, Lu Z (2018) Long non-coding RNA NEAT1 mediates the toxic of Parkinson’s disease induced by MPTP/MPP+ via regulation of gene expression. Clin Exp Pharmacol Physiol 45(8):841–848. https://doi.org/10.1111/1440-1681.12932
Liu Y, Zhao M (2016) lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes. Bioinformatics 32(10):1595–1597. https://doi.org/10.1093/bioinformatics/btw017
Liu Y, Ding W, Yu W, Zhang Y, Ao X, Wang J (2021) Long non-coding RNAs: Biogenesis, functions, and clinical significance in gastric cancer. Mol Ther - Oncolytics 23:458–476. https://doi.org/10.1016/j.omto.2021.11.005
Liu Y-C, Li J-R, Sun C-H, Andrews E, Chao R-F, Lin F-M, Weng S-L, Hsu S-D, Huang C-C, Cheng C, Liu C-C, Huang H-D (2015) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 44(D1):D209–D215. https://doi.org/10.1093/nar/gkv940
Lodde V, Murgia G, Simula ER, Steri M, Floris M, Idda ML (2020) Long Noncoding RNAs and Circular RNAs in Autoimmune Diseases. Biomolecules 10(7):1044. https://doi.org/10.3390/biom10071044
Loher P, Rigoutsos I (2012) Interactive exploration of RNA22 microRNA target predictions. Bioinformatics 28(24):3322–3323. https://doi.org/10.1093/bioinformatics/bts615
Long B, Li N, Xu X-X, Li X-X, Xu X-J, Guo D, Zhang D, Wu Z-H, Zhang S-Y (2018) Long noncoding RNA FTX regulates cardiomyocyte apoptosis by targeting miR-29b-1-5p and Bcl2l2. Biochem Biophys Res Commun 495(1):312–318. https://doi.org/10.1016/j.bbrc.2017.11.030
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, Sullivan S, Bridge J, Magazine H, Syron J, Fleming J (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45(6):580–585. https://doi.org/10.1038/ng.2653
Lorenz R, Bernhart SH, Höner zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA package 2.0. Algorithms Mol Biol 6(1). https://doi.org/10.1186/1748-7188-6-26
Lu Y, Hou S, Huang D, Luo X, Zhang J, Chen J, and Xu W (2015) Expression profile analysis of circulating microRNAs and their effects on ion channels in Chinese atrial fibrillation patients. Int J Clin Exp Med 8(1):845–853. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358520/
Lu Y, Zhang Y, Wang N, Pan Z, Gao X, Zhang F, Zhang Y, Shan H, Luo X, Bai Y, Sun L, Song W, Xu C, Wang Z, Yang B (2010) MicroRNA-328 contributes to adverse electrical remodeling in atrial fibrillation. Circulation 122(23):2378–2387. https://doi.org/10.1161/CIRCULATIONAHA.110.958967
Lu Z, Zhang Q, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY (2016) RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell 165(5):1267–1279. https://doi.org/10.1016/j.cell.2016.04.028
Ludwig N, Leidinger P, Becker K, Backes C, Fehlmann T, Pallasch C, Rheinheimer S, Meder B, Stähler C, Meese E, Keller A (2016) Distribution of miRNA expression across human tissues. Nucleic Acids Res 44(8):3865–3877. https://doi.org/10.1093/nar/gkw116
Lulli V, Romania P, Morsilli O, Cianciulli P, Gabbianelli M, Testa U, Giuliani A, Marziali G (2013) MicroRNA-486-3p Regulates γ-Globin Expression in Human Erythroid Cells by Directly Modulating BCL11A. PLoS ONE 8(4):e60436. https://doi.org/10.1371/journal.pone.0060436
Luo X, Pan Z, Shan H, Xiao J, Sun X, Wang N, Lin H, Xiao L, Maguy A, Qi X-Y, Li Y, Gao X, Dong D, Zhang Y, Bai Y, Ai J, Sun L, Lu H, Luo X-Y, Wang Z (2013) MicroRNA-26 governs profibrillatory inward-rectifier potassium current changes in atrial fibrillation. J Clin Investig 123(5):1939–1951. https://doi.org/10.1172/jci62185
Ma J, Liu F, Du X, Ma D, Xiong L (2017) Changes in lncRNAs and related genes in β-thalassemia minor and β-thalassemia major. Frontiers of Medicine 11(1):74–86. https://doi.org/10.1007/s11684-017-0503-1
Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z (2019) LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res 47(D1):D128–D134. https://doi.org/10.1093/nar/gky960
Ma X-K, Xue W, Chen L-L, Yang L (2021) CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets. Methods 196:3–10. https://doi.org/10.1016/j.ymeth.2021.02.008
Magee R, Londin E, Rigoutsos I (2019) TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson’s disease. Parkinsonism Relat Disord 65:203–209. https://doi.org/10.1016/j.parkreldis.2019.05.035
Magrelli A, Azzalin G, Salvatore M, Viganotti M, Tosto F, Colombo T, Devito R, Di Masi A, Antoccia A, Lorenzetti S, Maranghi F, Mantovani A, Tanzarella C, Macino G, Taruscio D (2009) Altered microRNA Expression Patterns in Hepatoblastoma Patients. Transl Oncol 2(3):157–163. https://doi.org/10.1593/tlo.09124
Manca S, Magrelli A, Cialfi S, Lefort K, Ambra R, Alimandi M, Biolcati G, Uccelletti D, Palleschi C, Screpanti I, Candi E, Melino G, Salvatore M, Taruscio D, Talora C (2011) Oxidative stress activation of miR-125b is part of the molecular switch for Hailey-Hailey disease manifestation. Exp Dermatol 20(11):932–937. https://doi.org/10.1111/j.1600-0625.2011.01359.x
Mann M, Wright PR, Backofen R (2017) IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions. Nucleic Acids Res 45(W1):W435–W439. https://doi.org/10.1093/nar/gkx279
Mapleson D, Moxon S, Dalmay T, Moulton V (2013) MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome. J Exp Zool Part B Mol Dev Evol 320(1):47–56. https://doi.org/10.1002/jez.b.22483
Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R (2017) LncATLAS database for subcellular localization of long noncoding RNAs. RNA 23(7):1080–1087. https://doi.org/10.1261/rna.060814.117
Massone S, Vassallo I, Fiorino G, Castelnuovo M, Barbieri F, Borghi R, Tabaton M, Robello M, Gatta E, Russo C, Florio T, Dieci G, Cancedda R, Pagano A (2011) 17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease. Neurobiol Dis 41(2):308–317. https://doi.org/10.1016/j.nbd.2010.09.019
Matera AG, Terns RM, Terns MP (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8(3):209–220. https://doi.org/10.1038/nrm2124
Mattick JS (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2(11):986–991. https://doi.org/10.1093/embo-reports/kve230
Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5(4):316–323. https://doi.org/10.1038/nrg1321
McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32(Web Server):W20–W25. https://doi.org/10.1093/nar/gkh435
McHugh CA, Chen C-K, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521(7551):232–236. https://doi.org/10.1038/nature14443
McKiernan PJ, Molloy K, Cryan SA, McElvaney NG, Greene CM (2014) Long noncoding RNA are aberrantly expressed in vivo in the cystic fibrosis bronchial epithelium. Int J Biochem Cell Biol 52:184–191. https://doi.org/10.1016/j.biocel.2014.02.022
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333–338. https://doi.org/10.1038/nature11928
Mendell JR, Rodino-Klapac LR, Sahenk Z, Roush K, Bird L, Lowes LP, Alfano L, Gomez AM, Lewis S, Kota J, Malik V, Shontz K, Walker CM, Flanigan KM, Corridore M, Kean JR, Allen HD, Shilling C, Melia KR, Sazani P (2013) Eteplirsen for the treatment of Duchenne muscular dystrophy. Ann Neurol 74(5):637–647. https://doi.org/10.1002/ana.23982
Menne J, Eulberg D, Beyer D, Baumann M, Saudek F, Valkusz Z, Więcek A, Haller H (2016) C-C motif-ligand 2 inhibition with emapticap pegol (NOX-E36) in type 2 diabetic patients with albuminuria. Nephrol Dial Transplant gfv459. https://doi.org/10.1093/ndt/gfv459
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155–159. https://doi.org/10.1038/nrg2521
Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL (2011) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 30(1):99–104. https://doi.org/10.1038/nbt.2024
Mercuri E, Darras BT, Chiriboga CA, Day JW, Campbell C, Connolly AM, Iannaccone ST, Kirschner J, Kuntz NL, Saito K, Shieh PB, Tulinius M, Mazzone ES, Montes J, Bishop KM, Yang Q, Foster R, Gheuens S, Bennett CF, Farwell W (2018) Nusinersen versus Sham Control in Later-Onset Spinal Muscular Atrophy. N Engl J Med 378(7):625–635. https://doi.org/10.1056/nejmoa1710504
Meseguer S, Martínez-Zamora A, García-Arumí E, Andreu AL, Armengod M-E (2015) The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome. Hum Mol Genet 24(1):167–184. https://doi.org/10.1093/hmg/ddu427
Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ (2018) Higher-Order Organization Principles of Pre-translational mRNPs. Mol Cell 72(4):715-726.e3. https://doi.org/10.1016/j.molcel.2018.09.012
Mhuantong W, Wichadakul D (2009) MicroPC (μPC): A comprehensive resource for predicting and comparing plant microRNAs. BMC Genomics 10(1):366. https://doi.org/10.1186/1471-2164-10-366
Micheletti R, Plaisance I, Abraham BJ, Sarre A, Ting C-C, Alexanian M, Maric D, Maison D, Nemir M, Young RA, Schroen B, González A, Ounzain S, Pedrazzini T (2017) The long noncoding RNA Wisper controls cardiac fibrosis and remodeling. Sci Transl Med 9(395):eaai9118. https://doi.org/10.1126/scitranslmed.aai9118
Mizuno H, Nakamura A, Aoki Y, Ito N, Kishi S, Yamamoto K, Sekiguchi M, Takeda S, Hashido K (2011) Identification of Muscle-Specific MicroRNAs in Serum of Muscular Dystrophy Animal Models: Promising Novel Blood-Based Markers for Muscular Dystrophy. PLoS ONE 6(3):e18388. https://doi.org/10.1371/journal.pone.0018388
Mockler TC, Ecker JR (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85(1):1–15. https://doi.org/10.1016/j.ygeno.2004.10.005
Mohr SE, Smith JA, Shamu CE, Neumüller RA, Perrimon N (2014) RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol 15(9):591–600. https://doi.org/10.1038/nrm3860
Morf J, Wingett SW, Farabella I, Cairns J, Furlan-Magaril M, Jiménez-García LF, Liu X, Craig FF, Walker S, Segonds-Pichon A, Andrews S, Marti-Renom MA, Fraser P (2019) RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus. Nat Biotechnol 37(7):793–802. https://doi.org/10.1038/s41587-019-0166-3
Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15(6):423–437. https://doi.org/10.1038/nrg3722
Morrison TA, Wilcox I, Luo H-Y, Farrell JJ, Kurita R, Nakamura Y, Murphy GJ, Cui S, Steinberg MH, Chui DHK (2018) A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression. Blood Cells Mol Dis 69:1–9. https://doi.org/10.1016/j.bcmd.2017.11.003
Mus E, Hof PR, Tiedge H (2007) Dendritic BC200 RNA in aging and in Alzheimer’s disease. Proc Natl Acad Sci 104(25):10679–10684. https://doi.org/10.1073/pnas.0701532104
Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R (2015) Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs. Bioinformatics 31(13):2199–2201. https://doi.org/10.1093/bioinformatics/btv106
Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Cuvellier S, Harel-Bellan A (2006) The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation. Nat Cell Biol 8(3):278–284. https://doi.org/10.1038/ncb1373
Nalluri JJ, Barh D, Azevedo V, Ghosh P (2017) miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures. Sci Rep 7(1):39684. https://doi.org/10.1038/srep39684
Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 37(Web Server issue):W356-362. https://doi.org/10.1093/nar/gkp294
Narducci MG, Arcelli D, Picchio MC, Lazzeri C, Pagani E, Sampogna F, Scala E, Fadda P, Cristofoletti C, Facchiano A, Frontani M, Monopoli A, Ferracin M, Negrini M, Lombardo GA, Caprini E, Russo G (2011) MicroRNA profiling reveals that miR-21, miR486 and miR-214 are upregulated and involved in cell survival in Sézary syndrome. Cell Death Dis 2:e151. https://doi.org/10.1038/cddis.2011.32
Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25(10):1335–1337. https://doi.org/10.1093/bioinformatics/btp157
Nguyen TC, Cao X, Yu P, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S (2016) Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun 7:12023. https://doi.org/10.1038/ncomms12023
Nikaido I (2004) EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. Nucleic Acids Res 32(90001):548D – 551. https://doi.org/10.1093/nar/gkh093
Oglesby IK, Chotirmall SH, McElvaney NG, Greene CM (2013) Regulation of Cystic Fibrosis Transmembrane Conductance Regulator by MicroRNA-145, -223, and -494 Is Altered in ΔF508 Cystic Fibrosis Airway Epithelium. J Immunol 190(7):3354–3362. https://doi.org/10.4049/jimmunol.1202960
Paco S, Casserras T, Rodríguez MA, Jou C, Puigdelloses M, Ortez CI, Diaz-Manera J, Gallardo E, Colomer J, Nascimento A, Kalko SG, Jimenez-Mallebrera C (2015) Transcriptome Analysis of Ullrich Congenital Muscular Dystrophy Fibroblasts Reveals a Disease Extracellular Matrix Signature and Key Molecular Regulators. PLoS ONE 10(12):e0145107. https://doi.org/10.1371/journal.pone.0145107
Pang KC (2004) RNAdb–a comprehensive mammalian noncoding RNA database. Nucleic Acids Res 33(Database issue):D125–D130. https://doi.org/10.1093/nar/gki089
Pantano L, Estivill X, Martí E (2009) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res 38(5):e34–e34. https://doi.org/10.1093/nar/gkp1127
Panwar B, Omenn GS, Guan Y (2017) miRmine: a database of human miRNA expression profiles. Bioinformatics btx019. https://doi.org/10.1093/bioinformatics/btx019
Park EJ, Choi J, Lee KC, Na DH (2019) Emerging PEGylated non-biologic drugs. Expert Opin Emerg Drugs 24(2):107–119. https://doi.org/10.1080/14728214.2019.1604684
Pattnaik B, Patnaik N, Mittal S, Mohan A, Agrawal A, Guleria R, Madan K (2022) Micro RNAs as potential biomarkers in tuberculosis: A systematic review. Non-Coding RNA Res 7(1):16–26. https://doi.org/10.1016/j.ncrna.2021.12.005
Perry MM, Muntoni F (2016) Noncoding RNAs and Duchenne muscular dystrophy. Epigenomics 8(11):1527–1537. https://doi.org/10.2217/epi-2016-0088
Petazzi P, Sandoval J, Szczesna K, Jorge OC, Roa L, Sayols S, Gomez A, Huertas D, Esteller M (2013) Dysregulation of the long non-coding RNA transcriptome in a Rett syndrome mouse model. RNA Biol 10(7):1197–1203. https://doi.org/10.4161/rna.24286
Pierdomenico AM, Patruno S, Codagnone M, Simiele F, Mari VC, Plebani R, Recchiuti A, Romano M (2017) microRNA-181b is increased in cystic fibrosis cells and impairs lipoxin A4 receptor-dependent mechanisms of inflammation resolution and antimicrobial defense. Sci Rep 7(1):13519. https://doi.org/10.1038/s41598-017-14055-y
Pliatsika V, Loher P, Magee R, Telonis AG, Londin E, Shigematsu M, Kirino Y, Rigoutsos I (2017) MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res 46(D1):D152–D159. https://doi.org/10.1093/nar/gkx1075
Plowman T, Lagos D (2021) Non-Coding RNAs in COVID-19: Emerging Insights and Current Questions. Non-Coding RNA 7(3):54. https://doi.org/10.3390/ncrna7030054
Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A, Lockhart S, Perez JL, Pérez Marc G, Moreira ED, Zerbini C, Bailey R, Swanson KA, Roychoudhury S, Koury K, Li P, Kalina WV, Cooper D, Frenck RW, Hammitt LL, Türeci Ö (2020) Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N Engl J Med 383(27):2603–2615. https://doi.org/10.1056/nejmoa2034577
Polesskaya O, Kananykhina E, Roy-Engel AM, Nazarenko O, Kulemzina I, Baranova A, Vassetsky Y, Myakishev-Rempel M (2018) The role of Alu-derived RNAs in Alzheimer’s and other neurodegenerative conditions. Med Hypotheses 115:29–34. https://doi.org/10.1016/j.mehy.2018.03.008
Pradhan RK, Ramakrishna W (2022) Transposons: Unexpected players in cancer. Gene 808:145975. https://doi.org/10.1016/j.gene.2021.145975
Prajapati B, Fatma M, Maddhesiya P, Sodhi MK, Fatima M, Dargar T, Bhagat R, Seth P, Sinha S (2019) Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells. RNA Biol 16(1):13–24. https://doi.org/10.1080/15476286.2018.1553482
Preusse M, Theis FJ, Mueller NS (2016) miTALOS v2: Analyzing Tissue Specific microRNA Function. PLoS ONE 11(3):e0151771. https://doi.org/10.1371/journal.pone.0151771
Qian C, Ye Y, Mao H, Yao L, Sun X, Wang B, Zhang H, Xie L, Zhang H, Zhang Y, Zhang S, He X (2019) Downregulated lncRNA-SNHG1 enhances autophagy and prevents cell death through the miR-221/222 /p27/mTOR pathway in Parkinson’s disease. Exp Cell Res 384(1):111614. https://doi.org/10.1016/j.yexcr.2019.111614
Qin Y, Buermans HPJ, van Kester MS, van der Fits L, Out-Luiting JJ, Osanto S, Willemze R, Vermeer MH, Tensen CP (2012) Deep-sequencing analysis reveals that the miR-199a2/214 cluster within DNM3os represents the vast majority of aberrantly expressed microRNAs in Sézary syndrome. J Invest Dermatol 132(5):1520–1522. https://doi.org/10.1038/jid.2011.481
Quek XC, Thomson DW, Maag JLV, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME (2014) lncRNAdb v20: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 43(D1):D168–D173. https://doi.org/10.1093/nar/gku988
Ramachandran S, Karp PH, Jiang P, Ostedgaard LS, Walz AE, Fisher JT, Keshavjee S, Lennox KA, Jacobi AM, Rose SD, Behlke MA, Welsh MJ, Xing Y, McCray PB (2012) A microRNA network regulates expression and biosynthesis of wild-type and ΔF508 mutant cystic fibrosis transmembrane conductance regulator. Proc Natl Acad Sci USA 109(33):13362–13367. https://doi.org/10.1073/pnas.1210906109
Ramsköld D, Luo S, Wang Y-C, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, Schroth GP, Sandberg R (2012) Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 30(8):777–782. https://doi.org/10.1038/nbt.2282
Reeves MB, Davies AA, McSharry BP, Wilkinson GW, Sinclair JH (2007) Complex I binding by a virally encoded RNA regulates mitochondria-induced cell death. Science (New York N.Y.) 316(5829):1345–1348. https://doi.org/10.1126/science.1142984
Reynolds RH, Petersen MH, Willert CW, Heinrich M, Nymann N, Dall M, Treebak JT, Björkqvist M, Silahtaroglu A, Hasholt L, Nørremølle A (2018) Perturbations in the p53/miR-34a/SIRT1 pathway in the R6/2 Huntington’s disease model. Mol Cell Neurosci 88:118–129. https://doi.org/10.1016/j.mcn.2017.12.009
Richardson PG, Smith AR, Triplett BM, Kernan NA, Grupp SA, Antin JH, Lehmann L, Shore T, Iacobelli M, Miloslavsky M, Hume R, Hannah AL, Nejadnik B, Soiffer RJ (2017) Defibrotide for Patients with Hepatic veno-occlusive disease/sinusoidal obstruction syndrome: interim results from a treatment IND study. Biol Blood Marrow Transplant 23(6):997–1004. https://doi.org/10.1016/j.bbmt.2017.03.008
Ritchie W, Flamant S, Rasko JEJ (2009) mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 26(2):223–227. https://doi.org/10.1093/bioinformatics/btp649
Robertson MP, Joyce GF (2010) The Origins of the RNA World. Cold Spring Harb Perspect Biol 4(5):a003608–a003608. https://doi.org/10.1101/cshperspect.a003608
Roy P, Bhattacharya G, Lahiri A, Dasgupta UB, Banerjee D, Chandra S, Das M (2012) hsa-miR-503 Is Downregulated in β Thalassemia Major. Acta Haematol 128(3):187–189. https://doi.org/10.1159/000339492
Ruan H, Xiang Y, Ko J, Li S, Jing Y, Zhu X, Ye Y, Zhang Z, Mills T, Feng J, Liu C-J, Jing J, Cao J, Zhou B, Wang L, Zhou Y, Lin C, Guo A-Y, Chen X, and Diao L (2019) Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines. Genome Med 11(1). https://doi.org/10.1186/s13073-019-0663-5
Ruffo P, Strafella C, Cascella R, Caputo V, Conforti FL, Andò S, Giardina E (2021) Deregulation of ncRNA in neurodegenerative disease: focus on circRNA, lncRNA and miRNA in amyotrophic lateral sclerosis. Front Genet 12. https://doi.org/10.3389/fgene.2021.784996
Russo F, Di Bella S, Nigita G, Macca V, Laganà A, Giugno R, Pulvirenti A, Ferro A (2012) miRandola: extracellular circulating microRNAs database. PLoS ONE 7(10):e47786. https://doi.org/10.1371/journal.pone.0047786
Saayman SM, Ackley A, Burdach J, Clemson M, Gruenert DC, Tachikawa K, Chivukula P, Weinberg MS, Morris KV (2016) Long non-coding RNA bgas regulates the cystic fibrosis transmembrane conductance regulator. Mol Ther 24(8):1351–1357. https://doi.org/10.1038/mt.2016.112
Sablok G, Milev I, Minkov G, Minkov I, Varotto C, Yahubyan G, Baev V (2013) isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett 587(16):2629–2634. https://doi.org/10.1016/j.febslet.2013.06.047
Sahin U, Oehm P, Derhovanessian E, Jabulowsky RA, Vormehr M, Gold M, Maurus D, Schwarck-Kokarakis D, Kuhn AN, Omokoko T, Kranz LM, Diken M, Kreiter S, Haas H, Attig S, Rae R, Cuk K, Kemmer-Brück A, Breitkreuz A, Tolliver C (2020) An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma. Nature 585(7823):107–112. https://doi.org/10.1038/s41586-020-2537-9
Saki N, Abroun S, Soleimani M, Kavianpour M, Shahjahani M, Mohammadi-Asl J, Hajizamani S (2016) MicroRNA expression in β-thalassemia and sickle cell disease: a role in the induction of fetal hemoglobin. Cell J 17(4):583–592. https://doi.org/10.22074/cellj.2016.3808
Sakurai M, Yano T, Kawabata H, Ueda H, Suzuki T (2010) Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol 6(10):733–740. https://doi.org/10.1038/nchembio.434
Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C (2010) MAGIA, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Res 38(Web Server):W352–W359. https://doi.org/10.1093/nar/gkq423
Salta E, De Strooper B (2017) Noncoding RNAs in neurodegeneration. Nat Rev Neurosci 18(10):627–640. https://doi.org/10.1038/nrn.2017.90
Salvatore M, Magrelli A, Taruscio D (2011) The role of microRNAs in the biology of rare diseases. Int J Mol Sci 12(10):6733–6742. https://doi.org/10.3390/ijms12106733
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7(2):e30733. https://doi.org/10.1371/journal.pone.0030733
Sang Q, Liu X, Wang L, Qi L, Sun W, Wang W, Sun Y, Zhang H (2018) CircSNCA downregulation by pramipexole treatment mediates cell apoptosis and autophagy in Parkinson’s disease by targeting miR-7. Aging 10(6):1281–1293. https://doi.org/10.18632/aging.101466
Santos RD, Raal FJ, Donovan JM, Cromwell WC (2015) Mipomersen preferentially reduces small low-density lipoprotein particle number in patients with hypercholesterolemia. J Clin Lipidol 9(2):201–209. https://doi.org/10.1016/j.jacl.2014.12.008
Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR (2013) Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non genetic gene-expression heterogeneity. Genome Biol 14(4). https://doi.org/10.1186/gb-2013-14-4-r31
Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T (2018) nextPARS: parallel probing of RNA structures in Illumina. RNA 24(4):609–619. https://doi.org/10.1261/rna.063073.117
Scaglioni D, Catapano F, Ellis M, Torelli S, Chambers D, Feng L, Beck M, Sewry C, Monforte M, Harriman S, Koenig E, Malhotra J, Popplewell L, Guglieri M, Straub V, Mercuri E, Servais L, Phadke R, Morgan J, Muntoni F (2021) The administration of antisense oligonucleotide golodirsen reduces pathological regeneration in patients with Duchenne muscular dystrophy. Acta Neuropathol Commun 9(1). https://doi.org/10.1186/s40478-020-01106-1
Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD (2018) timelapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nat Methods 15(3):221–225. https://doi.org/10.1038/nmeth.4582
Schultheis B, Strumberg D, Kuhlmann J, Wolf M, Link K, Seufferlein T, Kaufmann J, Feist M, Gebhardt F, Khan M, Stintzing S, Pelzer U (2020) Safety, efficacy and pharcacokinetics of targeted therapy with the liposomal rna interference therapeutic Atu027 Combined with gemcitabine in patients with pancreatic adenocarcinoma. a randomized phase Ib/IIa study. Cancers 12(11):3130. https://doi.org/10.3390/cancers12113130
Schultheis B, Strumberg D, Santel A, Vank C, Gebhardt F, Keil O, Lange C, Giese K, Kaufmann J, Khan M, Drevs J (2014) First-in-human phase i study of the liposomal RNA interference therapeutic Atu027 in patients with advanced solid tumors. J Clin Oncol 32(36):4141–4148. https://doi.org/10.1200/jco.2013.55.0376
Sekijima Y, Wiseman RL, Matteson J, Hammarström P, Miller SR, Sawkar AR, Balch WE, Kelly JW (2005) The biological and chemical basis for tissue-selective amyloid disease. Cell 121(1):73–85. https://doi.org/10.1016/j.cell.2005.01.018
Semenza GL (2014) Hypoxia-inducible factor 1 and cardiovascular disease. Annu Rev Physiol 76:39–56. https://doi.org/10.1146/annurev-physiol-021113-170322
Sethupathy P (2005) TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12(2):192–197. https://doi.org/10.1261/rna.2239606
Shan H, Zhang Y, Lu Y, Zhang Y, Pan Z, Cai B, Wang N, Li X, Feng T, Hong Y, Yang B (2009) Downregulation of miR-133 and miR-590 contributes to nicotine-induced atrial remodelling in canines. Cardiovasc Res 83(3):465–472. https://doi.org/10.1093/cvr/cvp130
Sharma E, Sterne-Weiler T, O’Hanlon D, Blencowe BJ (2016) Global mapping of human RNA-RNA interactions. Mol Cell 62(4):618–626. https://doi.org/10.1016/j.molcel.2016.04.030
Shen C, Kong B, Liu Y, Xiong L, Shuai W, Wang G, Quan D, Huang H (2018) YY1-induced upregulation of lncRNA KCNQ1OT1 regulates angiotensin II-induced atrial fibrillation by modulating miR-384b/CACNA1C axis. Biochem Biophys Res Commun 505(1):134–140. https://doi.org/10.1016/j.bbrc.2018.09.064
Shirley M (2021) Casimersen: First Approval. Drugs. https://doi.org/10.1007/s40265-021-01512-2
Shuang C, Guo M, Wang C, Liu X, Liu Y, Wu X (2016) MiRTDL: A deep learning approach for miRNA target prediction. IEEE/ACM Trans Comput Biol Bioinforma 13(6):1161–1169. https://doi.org/10.1109/TCBB.2015.2510002
Sinha D, Sengupta D, Bandyopadhyay S (2017) ParSel: parallel selection of Micro-RNAs for survival classification in cancers. Molecular Informatics 36(7). https://doi.org/10.1002/minf.201600141
Siwaponanan P, Fucharoen S, Sirankapracha P, Winichagoon P, Umemura T, Svasti S (2016) Elevated levels of miR-210 correlate with anemia in β-thalassemia/HbE patients. Int J Hematol 104(3):338–343. https://doi.org/10.1007/s12185-016-2032-0
Slack FJ, Chinnaiyan AM (2019) The Role of Non-coding RNAs in Oncology. Cell 179(5):1033–1055. https://doi.org/10.1016/j.cell.2019.10.017
Song X, Zhang N, Han P, Moon B-S, Lai RK, Wang K, Lu W (2016) Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic Acids Res 44(9):e87–e87. https://doi.org/10.1093/nar/gkw075
Sonneville F, Ruffin M, Coraux C, Rousselet N, Le Rouzic P, Blouquit-Laye S, Corvol H, Tabary O (2017) MicroRNA-9 downregulates the ANO1 chloride channel and contributes to cystic fibrosis lung pathology. Nature. Communications 8(1). https://doi.org/10.1038/s41467-017-00813-z
Srinoun K, Nopparatana C, Wongchanchailert M, Fucharoen S (2017) MiR-155 enhances phagocytic activity of β-thalassemia/HbE monocytes via targeting of BACH1. Int J Hematol 106(5):638–647. https://doi.org/10.1007/s12185-017-2291-4
Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM (2019) QRNAS: software tool for refinement of nucleic acid structures. BMC Struct Biol 19(1). https://doi.org/10.1186/s12900-019-0103-1
Steegmaier M, Hoffmann M, Baum A, Lénárt P, Petronczki M, Krššák M, Gürtler U, Garin-Chesa P, Lieb S, Quant J, Grauert M, Adolf GR, Kraut N, Peters J-M, Rettig WJ (2007) BI 2536, a potent and selective inhibitor of polo-like kinase 1, inhibits tumor growth in vivo. Curr Biol 17(4):316–322. https://doi.org/10.1016/j.cub.2006.12.037
Stegmayer G, Yones C, Kamenetzky L, Milone DH (2017) High class-imbalance in pre-miRNA prediction: a novel approach based on deepSOM. IEEE/ACM Trans Comput Biol Bioinf 14(6):1316–1326. https://doi.org/10.1109/tcbb.2016.2576459
Sticht C, De La Torre C, Parveen A, Gretz N (2018) miRWalk: an online resource for prediction of microRNA binding sites. PLoS ONE 13(10):e0206239. https://doi.org/10.1371/journal.pone.0206239
Stocks MB, Moxon S, Mapleson D, Woolfenden HC, Mohorianu I, Folkes L, Schwach F, Dalmay T, Moulton V (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics 28(15):2059–2061. https://doi.org/10.1093/bioinformatics/bts311
Sun F, Guo Z, Zhang C, Che H, Gong W, Shen Z, Shi Y, and Ge S (2019) LncRNA NRON alleviates atrial fibrosis through suppression of M1 macrophages activated by atrial myocytes. Biosci Reports 39(11):BSR20192215. https://doi.org/10.1042/BSR20192215
Sun K, Chen X, Jiang P, Song X, Wang H, Sun H (2013) iSeeRNA: identification of long intergenic noncoding RNA transcripts from transcriptome sequencing data. BMC Genomics 14(S2). https://doi.org/10.1186/1471-2164-14-s2-s7
Sun L, Liu H, Zhang L, Meng J (2015) lncRScan-SVM: a tool for predicting long non-coding RNAs using support vector machine. PLoS ONE 10(10):e0139654. https://doi.org/10.1371/journal.pone.0139654
Sun L, Sun S, Zeng S, Li Y, Pan W, Zhang Z (2015) Expression of circulating microRNA-1 and microRNA-133 in pediatric patients with tachycardia. Mol Med Rep 11(6):4039–4046. https://doi.org/10.3892/mmr.2015.3246
Sun Z, Nie X, Sun S, Dong S, Yuan C, Li Y, Xiao B, Jie D, Liu Y (2017) Long non-coding RNA MEG3 downregulation triggers human pulmonary artery smooth muscle cell proliferation and migration via the p53 signaling pathway. Cellul Physiol Biochem 42(6):2569–2581. https://doi.org/10.1159/000480218
Sweeney BA, Petrov AI, Burkov B, Finn RD, Bateman A, Szymanski M, Karlowski WM, Gorodkin J, Seemann SE, Cannone JJ, Gutell RR, Fey P, Basu S, Kay S, Cochrane G, Billis K, Emmert D, Marygold SJ, Huntley RP, Lovering RC (2018) RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 47(D1):D221–D229. https://doi.org/10.1093/nar/gky1034
Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462(7274):799–802. https://doi.org/10.1038/nature08618
Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J (2015) Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol 16(1). https://doi.org/10.1186/s13059-015-0690-5
Szcześniak MW, Makałowska I (2013) miRNEST 2.0: a database of plant and animal microRNAs. Nucleic Acids Res 42(D1):D74–D77. https://doi.org/10.1093/nar/gkt1156
Szcześniak MW, Rosikiewicz W, Makałowska I (2015) CANTATAdb: a collection of plant long non-coding RNAs. Plant Cell Physiol 57(1):e8–e8. https://doi.org/10.1093/pcp/pcv201
Taliaferro JM, Wang ET, Burge CB (2014) Genomic analysis of RNA localization. RNA Biol 11(8):1040–1050. https://doi.org/10.4161/rna.32146
Tano K, Akimitsu N (2012) Long non-coding RNAs in cancer progression. Front Genet 3. https://doi.org/10.3389/fgene.2012.00219
Täubel J, Hauke W, Rump S, Viereck J, Batkai S, Poetzsch J, Rode L, Weigt H, Genschel C, Lorch U, Theek C, Levin AA, Bauersachs J, Solomon SD, Thum T (2020) Novel antisense therapy targeting microRNA-132 in patients with heart failure: results of a first-in-human Phase 1b randomized, double-blind, placebo-controlled study. Eur Heart J 42(2):178–188. https://doi.org/10.1093/eurheartj/ehaa898
The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. https://doi.org/10.1038/nature11247
Thum T, Condorelli G (2015) Long noncoding RNAs and microRNAs in cardiovascular pathophysiology. Circ Res 116(4):751–762. https://doi.org/10.1161/circresaha.116.303549
Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild A-C, Tsay M, Lu R, Jurisica I (2018) mirDIP 4.1—integrative database of human microRNA target predictions. Nucleic Acids Res 46(Database issue):D360–D370. https://doi.org/10.1093/nar/gkx1144
Tong X, Liu S (2019) CPPred: coding potential prediction based on the global description of RNA sequence. Nucleic Acids Res 47(8):e43–e43. https://doi.org/10.1093/nar/gkz087
Tong X, Gu P, Xu S, Lin X (2015) Long non-coding RNA-DANCR in human circulating monocytes: a potential biomarker associated with postmenopausal osteoporosis. Biosci Biotechnol Biochem 79(5):732–737. https://doi.org/10.1080/09168451.2014.998617
Tong Z, Cui Q, Wang J, Zhou Y (2019) TransmiR v2.0: an updated transcription factor-microRNA regulation database. Nucleic Acids Res 47(D1):D253–D258. https://doi.org/10.1093/nar/gky1023
Toraih EA, El-Wazir A, Alghamdi SA, Alhazmi AS, El-Wazir M, Abdel-Daim MM, Fawzy MS (2019) Association of long non-coding RNA MIAT and MALAT1 expression profiles in peripheral blood of coronary artery disease patients with previous cardiac events. Genet Mol Biol 42(3):509–518. https://doi.org/10.1590/1678-4685-gmb-2018-0185
Trajkovski M, Hausser J, Soutschek J, Bhat B, Akin A, Zavolan M, Heim MH, Stoffel M (2011) MicroRNAs 103 and 107 regulate insulin sensitivity. Nature 474(7353):649–653. https://doi.org/10.1038/nature10112
Triozzi P, Kooshki M, Alistar A, Bitting R, Neal A, Lametschwandtner G, and Loibner H (2015) Phase I clinical trial of adoptive cellular immunotherapy with APN401 in patients with solid tumors. J ImmunoTherapy Cancer, 3(S2). https://doi.org/10.1186/2051-1426-3-s2-p175
Twayana S, Legnini I, Cesana M, Cacchiarelli D, Morlando M, Bozzoni I (2013) Biogenesis and function of non-coding RNAs in muscle differentiation and in Duchenne muscular dystrophy. Biochem Soc Trans 41(4):844–849. https://doi.org/10.1042/BST20120353
Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A (2008) CID-miRNA: a web server for prediction of novel miRNA precursors in human genome. Biochem Biophys Res Commun 372(4):831–834. https://doi.org/10.1016/j.bbrc.2008.05.134
Urdinguio RG, Fernández AF, Lopez-Nieva P, Rossi S, Huertas D, Kulis M, Liu C-G, Croce CM, Calin GA, Esteller M (2010) Disrupted microRNA expression caused by Mecp2 loss in a mouse model of Rett syndrome. Epigenetics 5(7):656–663. https://doi.org/10.4161/epi.5.7.13055
Uzilov AV, Underwood JG (2016) High-throughput nuclease probing of RNA structures using FragSeq. Methods Mol Biol (Clifton N.J.) 1490:105–134. https://doi.org/10.1007/978-1-4939-6433-8_8
van Rooij E (2011) The Art of MicroRNA Research. Circ Res 108(2):219–234. https://doi.org/10.1161/circresaha.110.227496
van Rooij E, Sutherland LB, Thatcher JE, DiMaio JM, Naseem RH, Marshall WS, Hill JA, Olson EN (2008) Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis. Proc Natl Acad Sci 105(35):13027–13032. https://doi.org/10.1073/pnas.0805038105
van Zandwijk N, Pavlakis N, Kao SC, Linton A, Boyer MJ, Clarke S, Huynh Y, Chrzanowska A, Fulham MJ, Bailey DL, Cooper WA, Kritharides L, Ridley L, Pattison ST, MacDiarmid J, Brahmbhatt H, Reid G (2017) Safety and activity of microRNA-loaded minicells in patients with recurrent malignant pleural mesothelioma: a first-in-man, phase 1, open-label, dose-escalation study. Lancet Oncol 18(10):1386–1396. https://doi.org/10.1016/S1470-2045(17)30621-6
Vausort M, Wagner DR, Devaux Y (2014) Long noncoding RNAs in patients with acute myocardial infarction. Circ Res 115(7):668–677. https://doi.org/10.1161/circresaha.115.303836
Viereck J, Kumarswamy R, Foinquinos A, Xiao K, Avramopoulos P, Kunz M, Dittrich M, Maetzig T, Zimmer K, Remke J, Just A, Fendrich J, Scherf K, Bolesani E, Schambach A, Weidemann F, Zweigerdt R, de Windt LJ, Engelhardt S, Dandekar T (2016) Long noncoding RNA Chast promotes cardiac remodeling. Sci Transl Med 8(326). https://doi.org/10.1126/scitranslmed.aaf1475
Vitravene Study Group (2002) A randomized controlled clinical trial of intravitreous fomivirsen for treatment of newly diagnosed peripheral cytomegalovirus retinitis in patients with AIDS. Am J Ophthalmol 133(4):467–474. https://doi.org/10.1016/s0002-9394(02)01327-2
Vitsios DM, Enright AJ (2015) Chimira: analysis of small RNA sequencing data and microRNA modifications: Fig. 1. Bioinformatics 31(20):3365–3367. https://doi.org/10.1093/bioinformatics/btv380
Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ (2017) Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests. Nucleic Acids Res 45(21):e177. https://doi.org/10.1093/nar/gkx836
Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG (2015) DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Research 43(W1):W460–W466. https://doi.org/10.1093/nar/gkv403
Volders P-J, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P (2012) LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 41(D1):D246–D251. https://doi.org/10.1093/nar/gks915
Wan C, Gao J, Zhang H, Jiang X, Zang Q, Ban R, Zhang Y, Shi Q (2017) CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data. Bioinformatics 33(20):3289–3291. https://doi.org/10.1093/bioinformatics/btx066
Wang C, Wei L, Guo M, Zou Q (2013) Computational approaches in detecting non- coding RNA. Curr Genomics 14(6):371–377. https://doi.org/10.2174/13892029113149990005
Wang H, Song T, Zhao Y, Zhao J, Wang X, Fu X (2020) Long non-coding RNA LICPAR regulates atrial fibrosis via TGF-β/Smad pathway in atrial fibrillation. Tissue Cell 67:101440. https://doi.org/10.1016/j.tice.2020.101440
Wang K, Liu C-Y, Zhou L-Y, Wang J-X, Wang M, Zhao B, Zhao W-K, Xu S-J, Fan L-H, Zhang X-J, Feng C, Wang C-Q, Zhao Y-F, and Li P-F (2015) APF lncRNA regulates autophagy and myocardial infarction by targeting miR-188–3p. Nat Commun 6(1). https://doi.org/10.1038/ncomms7779
Wang K, Liu F, Liu C-Y, An T, Zhang J, Zhou L-Y, Wang M, Dong Y-H, Li N, Gao J-N, Zhao Y-F, Li P-F (2016) The long noncoding RNA NRF regulates programmed necrosis and myocardial injury during ischemia and reperfusion by targeting miR-873. Cell Death Differ 23(8):1394–1405. https://doi.org/10.1038/cdd.2016.28
Wang K, Liu F, Zhou L-Y, Long B, Yuan S-M, Wang Y, Liu C-Y, Sun T, Zhang X-J, Li P-F (2014) The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 114(9):1377–1388. https://doi.org/10.1161/circresaha.114.302476
Wang K, Long B, Zhou L-Y, Liu F, Zhou Q-Y, Liu C-Y, Fan Y-Y, and Li P-F (2014b) CARL lncRNA inhibits anoxia-induced mitochondrial fission and apoptosis in cardiomyocytes by impairing miR-539-dependent PHB2 downregulation. Nat Commun 5(1). https://doi.org/10.1038/ncomms4596
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38(18):e178–e178. https://doi.org/10.1093/nar/gkq622
Wang K, Sun T, Li N, Wang Y, Wang J-X, Zhou L-Y, Long B, Liu C-Y, Liu F, Li P-F (2014) MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361. PLoS Genet 10(7):e1004467. https://doi.org/10.1371/journal.pgen.1004467
Wang L, Liu Y, Zhong X, Liu H, Lu C, Li C, Zhang H (2019) DMfold: a novel method to predict RNA secondary structure with pseudoknots based on deep learning and improved base pair maximization principle. Front Genet 10:143. https://doi.org/10.3389/fgene.2019.00143
Wang L, Zhou L, Jiang P, Lu L, Chen X, Lan H, Guttridge DC, Sun H, Wang H (2012) Loss of miR-29 in myoblasts contributes to dystrophic muscle pathogenesis. Mol Ther 20(6):1222–1233. https://doi.org/10.1038/mt.2012.35
Wang S, Zhang X, Guo Y, Rong H, Liu T (2017) The long noncoding RNA HOTAIR promotes Parkinson’s disease by upregulating LRRK2 expression. Oncotarget 8(15):24449–24456. https://doi.org/10.18632/oncotarget.15511
Wang W, Wang X, Zhang Y, Li Z, Xie X, Wang J, Gao M, Zhang S, Hou Y (2015) Transcriptome analysis of canine cardiac fat pads: involvement of two novel long non-coding RNAs in atrial fibrillation neural remodeling. J Cell Biochem 116(5):809–821. https://doi.org/10.1002/jcb.25037
Wang W, Zhuang Q, Ji K, Wen B, Lin P, Zhao Y, Li W, Yan C (2017) Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation. Sci Rep 7:41639. https://doi.org/10.1038/srep41639
Wang X (2008) miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA 14(6):1012–1017. https://doi.org/10.1261/rna.965408
Wang X, Yong C, Yu K, Yu R, Zhang R, Yu L, Li S, Cai S (2018) Long noncoding RNA (lncRNA) n379519 promotes cardiac fibrosis in post-infarct myocardium by targeting miR-30. Med Sci Monitor 24:3958–3965. https://doi.org/10.12659/msm.910000
Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21(18):3610–3614. https://doi.org/10.1093/bioinformatics/bti562
Wang X, Zhang M, Liu H (2019) LncRNA17A regulates autophagy and apoptosis of SH-SY5Y cell line as an in vitro model for Alzheimer’s disease. Biosci Biotechnol Biochem 83(4):609–621. https://doi.org/10.1080/09168451.2018.1562874
Wang X, Zhao Z, Zhang W, Wang Y (2018) Long noncoding RNA LINC00968 promotes endothelial cell proliferation and migration via regulating miR-9-3p expression. J Cell Biochem. https://doi.org/10.1002/jcb.28103
Wang X-M, Li X-M, Song N, Zhai H, Gao X-M, Yang Y-N (2019) Long non-coding RNAs H19, MALAT1 and MIAT as potential novel biomarkers for diagnosis of acute myocardial infarction. Biomed Pharmacother=Biomedecine & Pharmacotherapie 118:109208. https://doi.org/10.1016/j.biopha.2019.109208
Wang Y-N-Z, Shan K, Yao M-D, Yao J, Wang J-J, Li X, Liu B, Zhang Y-Y, Ji Y, Jiang Q, Yan B (2016) Long Noncoding RNA-GAS5. Hypertension 68(3):736–748. https://doi.org/10.1161/hypertensionaha.116.07259
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. https://doi.org/10.1038/nrg2484
Wang Z, Zhang X-J, Ji Y-X, Zhang P, Deng K-Q, Gong J, Ren S, Wang X, Chen I, Wang H, Gao C, Yokota T, Ang YS, Li S, Cass A, Vondriska TM, Li G, Deb A, Srivastava D, Yang H-T (2016) The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. Nat Med 22(10):1131–1139. https://doi.org/10.1038/nm.4179
Washietl S (2007) Prediction of structural noncoding RNAs with RNAz. Methods Mol Biol 395:503–526. https://doi.org/10.1007/978-1-59745-514-5_32
Wen X, Gao L, Guo X, Li X, Huang X, Wang Y, Xu H, He R, Jia C, Liang F (2018) lncSLdb: a resource for long non-coding RNA subcellular localization. Database 2018. https://doi.org/10.1093/database/bay085
Wheeler TM, Leger AJ, Pandey SK, MacLeod AR, Nakamori M, Cheng SH, Wentworth BM, Bennett CF, Thornton CA (2012) Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 488(7409):111–115. https://doi.org/10.1038/nature11362
Widera C, Gupta SK, Lorenzen JM, Bang C, Bauersachs J, Bethmann K, Kempf T, Wollert KC, Thum T (2011) Diagnostic and prognostic impact of six circulating microRNAs in acute coronary syndrome. J Mol Cell Cardiol 51(5):872–875. https://doi.org/10.1016/j.yjmcc.2011.07.011
Wilkinson KA, Merino EJ, Weeks KM (2006) Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 1(3):1610–1616. https://doi.org/10.1038/nprot.2006.249
Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R, Sanes JR, Olson EN (2009) MicroRNA-206 Delays ALS Progression and Promotes Regeneration of Neuromuscular Synapses in Mice. Science 326(5959):1549–1554. https://doi.org/10.1126/science.1181046
Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23(13):1494–1504. https://doi.org/10.1101/gad.1800909
Winkle M, El-Daly SM, Fabbri M, Calin GA (2021) Noncoding RNA therapeutics — challenges and potential solutions. Nat Rev Drug Discovery. https://doi.org/10.1038/s41573-021-00219-z
Wong NW, Chen Y, Chen S, Wang X (2018) OncomiR: an online resource for exploring pan-cancer microRNA dysregulation. Bioinforma (Oxford England) 34(4):713–715. https://doi.org/10.1093/bioinformatics/btx627
Wu H, Zhao Z-A, Liu J, Hao K, Yu Y, Han X, Li J, Wang Y, Lei W, Dong N, Shen Z, Hu S (2018) Long noncoding RNA Meg3 regulates cardiomyocyte apoptosis in myocardial infarction. Gene Ther 25(8):511–523. https://doi.org/10.1038/s41434-018-0045-4
Wu W, Ji P, and Zhao F (2020) CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biol 21(1). https://doi.org/10.1186/s13059-020-02018-y
Wu X, Pan Y, Fang Y, Zhang J, Xie M, Yang F, Yu T, Ma P, Li W, Shu Y (2020) The biogenesis and functions of piRNAs in human diseases. Mol Ther - Nucleic Acids 21:108–120. https://doi.org/10.1016/j.omtn.2020.05.023
Wu Y-Y, and Kuo H-C (2020) Functional roles and networks of non-coding RNAs in the pathogenesis of neurodegenerative diseases. J Biomed Sci 27(1). https://doi.org/10.1186/s12929-020-00636-z
Wu Y-Y, Chiu F-L, Yeh C-S, Kuo H-C (2019) Opportunities and challenges for the use of induced pluripotent stem cells in modelling neurodegenerative disease. Open Biol 9(1). https://doi.org/10.1098/rsob.180177
Xia S, Feng J, Chen K, Ma Y, Gong J, Cai F, Jin Y, Gao Y, Xia L, Chang H, Wei L, Han L, He C (2018) CSCD: a database for cancer-specific circular RNAs. Nucleic Acids Res 46(D1):D925–D929. https://doi.org/10.1093/nar/gkx863
Xia S, Feng J, Lei L, Hu J, Xia L, Wang J, Xiang Y, Liu L, Zhong S, Han L, He C (2016) Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. Brief Bioinform bbw081. https://doi.org/10.1093/bib/bbw081
Xiao F, Zuo Z, Cai G, Kang S, Gao X, and Li T (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37(Database):D105–D110. https://doi.org/10.1093/nar/gkn851
Xie B, Ding Q, Han H, Wu D (2013) miRCancer: a microRNA-cancer association database constructed by text mining on literature. Bioinformatics 29(5):638–644. https://doi.org/10.1093/bioinformatics/btt014
Xiong G, Jiang X, Song T (2019) The overexpression of lncRNA H19 as a diagnostic marker for coronary artery disease. Revista Da Associacao Medica Brasileira (1992) 65(2):110–117. https://doi.org/10.1590/1806-9282.65.2.110
Xiong R, Wang Z, Zhao Z, Li H, Chen W, Zhang B, Wang L, Wu L, Li W, Ding J, Chen S (2014) MicroRNA-494 reduces DJ-1 expression and exacerbates neurodegeneration. Neurobiol Aging 35(3):705–714. https://doi.org/10.1016/j.neurobiolaging.2013.09.027
Xu Y, Zhou X, Zhang W (2008) MicroRNA prediction with a novel ranking algorithm based on random walks. Bioinforma (Oxford England) 24(13):i50-58. https://doi.org/10.1093/bioinformatics/btn175
Yan B, Wang Z-H, Guo J-T (2012) The research strategies for probing the function of long noncoding RNAs. Genomics 99(2):76–80. https://doi.org/10.1016/j.ygeno.2011.12.002
Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, Zhang Y, Yang L, Shan W, He Q, Fan L, Kandalaft LE, Tanyi JL, Li C, Yuan C-X, Zhang D, Yuan H, Hua K, Lu Y, Katsaros D (2015) Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell 28(4):529–540. https://doi.org/10.1016/j.ccell.2015.09.006
Yan Z, Huang N, Wu W, Chen W, Jiang Y, Chen J, Huang X, Wen X, Xu J, Jin Q, Zhang K, Chen Z, Chien S, Zhong S (2019) Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. Proc Natl Acad Sci USA 116(8):3328–3337. https://doi.org/10.1073/pnas.1819788116
Yan Z, McCray PB Jr, Engelhardt JF (2019) Advances in gene therapy for cystic fibrosis lung disease. Hum Mol Genet 28(R1):R88–R94. https://doi.org/10.1093/hmg/ddz139
Yang J-H, Zhang X-C, Huang Z-P, Zhou H, Huang M-B, Zhang S, Chen Y-Q, Qu L-H (2006) snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res 34(18):5112–5123. https://doi.org/10.1093/nar/gkl672
Yang K, Sablok G, Qiao G, Nie Q, Wen X (2017) isomiR2Function: An integrated workflow for identifying MicroRNA variants in plants. Front Plant Sci 08. https://doi.org/10.3389/fpls.2017.00322
Yang Y, Cai Y, Wu G, Chen X, Liu Y, Wang X, Yu J, Li C, Chen X, Jose PA, Zhou L, Zeng C (2015) Plasma long non-coding RNA, CoroMarker, a novel biomarker for diagnosis of coronary artery disease. Clin Sci 129(8):675–685. https://doi.org/10.1042/cs20150121
Yang Z, Ren F, Liu C, He S, Sun G, Gao Q, Yao L, Zhang Y, Miao R, Cao Y, Zhao Y, Zhong Y, Zhao H (2010) dbDEMC: a database of differentially expressed miRNAs in human cancers. BMC Genomics 11(S4). https://doi.org/10.1186/1471-2164-11-s4-s5
Yao L, Zhou B, You L, Hu H, Xie R (2020) LncRNA MIAT/miR-133a-3p axis regulates atrial fibrillation and atrial fibrillation-induced myocardial fibrosis. Mol Biol Rep. https://doi.org/10.1007/s11033-020-05347-0
Yi J, Chen B, Yao X, Lei Y, Ou F, Huang F (2019) Upregulation of the lncRNA MEG3 improves cognitive impairment, alleviates neuronal damage, and inhibits activation of astrocytes in hippocampus tissues in Alzheimer’s disease through inactivating the PI3K/Akt signaling pathway. J Cell Biochem. https://doi.org/10.1002/jcb.29108
You X, and Conrad TO (2016) Acfs: accurate circRNA identification and quantification from RNA-Seq data. Sci Reports 6(1). https://doi.org/10.1038/srep38820
Yu F, Zhang G, Shi A, Hu J, Li F, Zhang X, Zhang Y, Huang J, Xiao Y, Li X, Cheng S (2018) LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse. Database 2018. https://doi.org/10.1093/database/bay039
Yuan C, Sun Y (2013) RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes. PLoS ONE 8(10):e77596. https://doi.org/10.1371/journal.pone.0077596
Yuasa K, Hagiwara Y, Ando M, Nakamura A, Takeda S, Hijikata T (2008) MicroRNA-206 is highly expressed in newly formed muscle fibers: implications regarding potential for muscle regeneration and maturation in muscular dystrophy. Cell Struct Funct 33(2):163–169. https://doi.org/10.1247/csf.08022
Zaharieva IT, Calissano M, Scoto M, Preston M, Cirak S, Feng L, Collins J, Kole R, Guglieri M, Straub V, Bushby K, Ferlini A, Morgan JE, Muntoni F (2013) Dystromirs as serum biomarkers for monitoring the disease severity in Duchenne muscular Dystrophy. PLoS ONE 8(11):e80263. https://doi.org/10.1371/journal.pone.0080263
Zangrando J, Zhang L, Vausort M, Maskali F, Marie P-Y, Wagner DR, Devaux Y (2014) Identification of candidate long non-coding RNAs in response to myocardial infarction. BMC Genomics 15(1). https://doi.org/10.1186/1471-2164-15-460
Zeller T, Keller T, Ojeda F, Reichlin T, Twerenbold R, Tzikas S, Wild PS, Reiter M, Czyz E, Lackner KJ, Munzel T, Mueller C, Blankenberg S (2014) Assessment of microRNAs in patients with unstable angina pectoris. Eur Heart J 35(31):2106–2114. https://doi.org/10.1093/eurheartj/ehu151
Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, … Wu Y (2021a) Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol Cancer 20(1):126. https://doi.org/10.1186/s12943-021-01431-6
Zhang J, Gao C, Meng M, Tang H (2016) Long noncoding RNA MHRT protects cardiomyocytes against H2O2-induced apoptosis. Biomol Ther 24(1):19–24. https://doi.org/10.4062/biomolther.2015.066
Zhang J, Yu L, Xu Y, Liu Y, Li Z, Xue X, Wan S, Wang H (2018) Long noncoding RNA upregulated in hypothermia treated cardiomyocytes protects against myocardial infarction through improving mitochondrial function. Int J Cardiol 266:213–217. https://doi.org/10.1016/j.ijcard.2017.12.097
Zhang S, Yue Y, Sheng L, Wu Y, Fan G, Li A, Hu X, ShangGuan M, Wei C (2013) PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress. BMC Plant Biol 13(1). https://doi.org/10.1186/1471-2229-13-33
Zhang T, Pang P, Fang Z, Guo Y, Li H, Li X, Tian T, Yang X, Chen W, Shu S, Tang N, Wu J, Zhu H, Pei L, Liu D, Tian Q, Wang J, Wang L, Zhu L-Q, Lu Y (2018) Expression of BC1 impairs spatial learning and memory in Alzheimer’s disease via APP translation. Mol Neurobiol 55(7):6007–6020. https://doi.org/10.1007/s12035-017-0820-z
Zhang T-N, Li D, Xia J, Wu Q-J, Wen R, Yang N, Liu C-F (2017) Non-coding RNA: a potential biomarker and therapeutic target for sepsis. Oncotarget 8(53):91765–91778. https://doi.org/10.18632/oncotarget.21766
Zhang W, Liu Y, Min Z, Liang G, Mo J, Ju Z, Zeng B, Guan W, Zhang Y, Chen J, Zhang Q, Li H, Zeng C, Wei Y, Chan G-F (2021) circMine: a comprehensive database to integrate, analyze and visualize human disease–related circRNA transcriptome. Nucleic Acids Res 50(D1):D83–D92. https://doi.org/10.1093/nar/gkab809
Zhang W, Yue X, Tang G, Wu W, Huang F, Zhang X (2018) SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions. PLoS Comput Biol 14(12):e1006616. https://doi.org/10.1371/journal.pcbi.1006616
Zhang Y, Sun L, Xuan L, Pan Z, Li K, Liu S, Huang Y, Zhao X, Huang L, Wang Z, Hou Y, Li J, Tian Y, Yu J, Han H, Liu Y, Gao F, Zhang Y, Wang S, Du Z (2016) Reciprocal changes of circulating long non-coding RNAs ZFAS1 and CDR1AS predict acute myocardial infarction. Sci Rep 6:22384. https://doi.org/10.1038/srep22384
Zhang Y, Zang Q, Xu B, Zheng W, Ban R, Zhang H, Yang Y, Hao Q, Iqbal F, Li A, Shi Q (2016) IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 32(13):2069–2071. https://doi.org/10.1093/bioinformatics/btw070
Zhang Y, Zheng S, Geng Y, Xue J, Wang Z, Xie X, Wang J, Zhang S, Hou Y (2015) MicroRNA profiling of atrial fibrillation in canines: miR-206 modulates intrinsic cardiac autonomic nerve remodeling by regulating SOD1. PLoS ONE 10(3):e0122674. https://doi.org/10.1371/journal.pone.0122674
Zhang Z, Cheng Y (2014) miR-16-1 promotes the aberrantα-synuclein accumulation in parkinson disease via targeting heat shock protein 70. Sci World J 2014:1–8. https://doi.org/10.1155/2014/938348
Zhang Z, Gao W, Long Q-Q, Zhang J, Li Y-F, Liu D-C, Yan J-J, Yang Z-J, Wang L-S (2017) Increased plasma levels of lncRNA H19 and LIPCAR are associated with increased risk of coronary artery disease in a Chinese population. Sci Rep 7(1):7491. https://doi.org/10.1038/s41598-017-07611-z
Zhao L, Ma Z, Guo Z, Zheng M, Li K, Yang X (2020) Analysis of long non-coding RNA and mRNA profiles in epicardial adipose tissue of patients with atrial fibrillation. Biomed Pharmacother = Biomedecine & Pharmacotherapie 121:109634. https://doi.org/10.1016/j.biopha.2019.109634
Zhao S, Li S, Liu W, Wang Y, Li X, Zhu S, Lei X, Xu S (2020) Circular RNA signature in lung adenocarcinoma: a mioncocirc database-based study and literature review. Front Oncol 10:523342. https://doi.org/10.3389/fonc.2020.523342
Zheng L-L, Xu W-L, Liu S, Sun W-J, Li J-H, Wu J, Yang J-H, Qu L-H (2016) tRF2Cancer: a web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res 44(W1):W185-193. https://doi.org/10.1093/nar/gkw414
Zhou K-R, Liu S, Sun W-J, Zheng L-L, Zhou H, Yang J-H, Qu L-H (2017) ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res 45(D1):D43–D50. https://doi.org/10.1093/nar/gkw965
Zhou M, Zou Y-G, Xue Y-Z, Wang X-H, Gao H, Dong H-W, Zhang Q (2018) Long non-coding RNA H19 protects acute myocardial infarction through activating autophagy in mice. European Rev Med Pharmacol Sci 22(17):5647–5651. https://doi.org/10.26355/eurrev_201809_15831
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 38(suppl_2):W392–W397. https://doi.org/10.1093/nar/gkq393
Zorde Khvalevsky E, Gabai R, Rachmut IH, Horwitz E, Brunschwig Z, Orbach A, Shemi A, Golan T, Domb AJ, Yavin E, Giladi H, Rivkin L, Simerzin A, Eliakim R, Khalaileh A, Hubert A, Lahav M, Kopelman Y, Goldin E, Dancour A (2013) Mutant KRAS is a druggable target for pancreatic cancer. Proc Natl Acad Sci 110(51):20723–20728. https://doi.org/10.1073/pnas.1314307110
Zou Q, Lin C, Liu X-Y, Han Y-P, Li W-B, Guo M-Z (2011) Novel representation of RNA secondary structure used to improve prediction algorithms. Genet Mol Res: GMR 10(3):1986–1998. https://doi.org/10.4238/vol10-3gmr1181
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415. https://doi.org/10.1093/nar/gkg595
Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9(1):133–148. https://doi.org/10.1093/nar/9.1.133
Zuntini M, Salvatore M, Pedrini E, Parra A, Sgariglia F, Magrelli A, Taruscio D, Sangiorgi L (2010) MicroRNA profiling of multiple osteochondromas: identification of disease-specific and normal cartilage signatures. Clin Genet 78(6):507–516. https://doi.org/10.1111/j.1399-0004.2010.01490.x
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The authors would like to thank the Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India, for providing the necessary research facilities and encouragement to carry out this work.
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Loganathan, T., Doss C, G.P. Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 23, 33 (2023). https://doi.org/10.1007/s10142-022-00947-4
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DOI: https://doi.org/10.1007/s10142-022-00947-4