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Review

Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells

by
Pouneh Maraghechi
1,†,
Maria Teresa Salinas Aponte
1,†,
András Ecker
1,
Bence Lázár
1,2,
Roland Tóth
1,
Nikolett Tokodyné Szabadi
1 and
Elen Gócza
1,*
1
Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
2
National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation (NBGK-HGI), Isaszegi str. 200, 2100 Gödöllő, Hungary
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2023, 14(7), 1434; https://doi.org/10.3390/genes14071434
Submission received: 20 May 2023 / Revised: 6 July 2023 / Accepted: 7 July 2023 / Published: 12 July 2023
(This article belongs to the Special Issue RNA Interference Pathways, Volume II)
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Abstract

:
MicroRNAs (miRNAs), small non-coding RNA molecules, regulate a wide range of critical biological processes, such as proliferation, cell cycle progression, differentiation, survival, and apoptosis, in many cell types. The regulatory functions of miRNAs in embryogenesis and stem cell properties have been extensively investigated since the early years of miRNA discovery. In this review, we will compare and discuss the impact of stem-cell-specific miRNA clusters on the maintenance and regulation of early embryonic development, pluripotency, and self-renewal of embryonic stem cells, particularly in vertebrates.

1. Introduction

microRNAs (miRNAs) are endogenous, 22–25 nucleotide long non-coding RNAs that post-transcriptionally regulate gene expression by binding to the 3′ untranslated region (UTR) of their target mRNAs and inhibiting their translation or stability. The central regulatory role of miRNAs in multiple biological processes, including cell cycle regulation, apoptosis, aging, cell fate decisions, and different signaling pathways, has been widely described. Developmental studies in vertebrates demonstrated that miRNAs are crucial molecules for embryogenesis (reviewed by [1,2]). Indeed, miRNAs play important roles in stem cell properties by regulating self-renewal and differentiation (reviewed by [3,4]). In this review, we will focus on the impact of stem-cell-specific miRNA clusters on the maintenance and regulation of early embryogenesis and embryonic stem cell (ESC) pluripotency in vertebrates, particularly in humans, mice, rabbits, and chickens.

2. Overview of microRNA Biogenesis

miRNA genes are transcribed by RNA Polymerase II/III into long primary transcripts (pri-miRNA), which can also be polycistronic [5,6]. A significant percentage of miRNAs are intragenic, residing within their host gene’s intronic or/and exonic regions [7]. They are transcribed from introns, and occasionally from exons of protein-coding genes, sharing the host gene’s expression regulators. Conversely, intergenic miRNAs are located between genes and transcribed independently from their own promoters [6,8]. However, some intergenic miRNAs can also be co-transcribed with their neighboring genes [9]. Many miRNAs are localized as a cluster on the same chromosome in a close proximity of maximum 10 kb [10,11]. They are co-transcribed from the same genomic loci as a single polycistronic transcript [12,13]. They also share the same seed sequence, therefore sharing common target mRNAs and biological functions [10,14]. The biogenesis of miRNA can follow canonical or non-canonical pathways.
In the canonical pathway, pri-miRNAs are mostly transcribed by RNA Polymerase II [5]. Transcribed pri-miRNA forms a hairpin structure. This structure has two domains that are recognized by the Drosha microprocessor complex (composed of Drosha and Dgcr8). Drosha cleaves the stem of the hairpin and produces a shorter hairpin, termed “precursor miRNA” (pre-miRNA) [15]. In the presence of the RanGTP cofactor, Exportin-5 translocates the pre-miRNA from the nucleus into the cytoplasm where Dicer further cleaves it and generates a short, double-stranded miRNA precursor [16]. One of the strands of the generated miRNA duplex is selected as a guide miRNA by Argonaute based on the identities of the 5′ nucleotide of each strand and the relative thermodynamic stability of the two ends of the duplex, while the other strand (miRNA*) is degraded. The guide miRNA strand is then loaded into Argonaute 2 (AGO2), building the RISC complex which is composed of the RNAse III-type nuclease Dicer and the PAZ/PIWI protein (AGO2) [17,18,19]. Once miRISC is built, it can bind to its target mRNA’s 3′-UTR through a complementary sequence. A perfect base pairing results in target degradation, while an imperfect base pairing results in translational silencing of the target mRNA. The miRNA structure contains a well-conserved sequence of six nucleotides called the “seed” that represents the most important feature of target recognition [20,21].
Non-canonical miRNAs are also derived from RNA Polymerase II; however, few miRNAs can be transcribed from RNA Polymerase III. The non-canonical miRNA biogenesis occurs through a Drosha/Dgcr8 and/or Dicer-independent manner, when miRNAs originate from introns (mirtrons) [22,23] or other small RNAs, such as snoRNAs, shRNAs, tRNAs, tRNase Z, and endo-siRNAs [24,25,26,27,28]. miRNAs derived from endo-shRNAs and tRNA precursors are transcribed by RNA Polymerase III [24,27].
In the Drosha/ Dgcr8-independent pathway (also called the mirtron pathway), introns are primarily processed in the nucleus by the spliceosome and a debranching enzyme that produces short hairpins called mirtrons. These hairpins are then exported to the cytoplasm by Exportin-5 and cleaved by Dicer [22,23]. Even though the majority of introns in vertebrates are elongated from several kilobases up to megabases in length, there are short introns of 50–150 nt in length which may form hairpin structures [29,30]. Hence, mitrons constitute only a small fraction of mammalian miRNAs. There are other subclasses of miRNAs with a potential pre-miRNA-like hairpin which are derived by an alternative Drosha/ Dgcr8-independent pathway. The processing of snoRNAs, shRNAs, tRNAs, tRNase Z, and endo-siRNA precursors to miRNAs are also independent of Drosha/ Dgcr8 [24,25,26,27,28].
In the Dicer-independent pathway, the produced pri-miRNAs are processed by Drosha into pre-miRNAs. However, these pre-miRNAs are not suitable substrates for Dicer; therefore, they are loaded into Ago2 instead, and Ago2-dependent cleavage produces an intermediate 3′ end. The final maturation occurs as the 3′-5′ trimming of the 5′ strand is completed by a cellular nuclease [31,32]. In the Dicer-independent pathway, the tRNase Z-dependent pathway precursor tRNA is cleaved by tRNase Z at the 3′ end [33].

3. Role of the miRNAs in Embryonic Development

Many miRNAs function during early embryonic development. The first known miRNA, lin-4, plays a crucial role in the developmental timing of stage-specific cell lineages in C. elegans [34]. Shortly after the discovery of lin-4, let-7 was recognized as an essential miRNA to control the pattern of temporal development of larval cell fates during the adult stage, which acts as a temporal switch between larval and adult fates. Loss of the let-7 gene activity leads to abnormalities in the pattern of larval development as a result of the reiteration of larval cell fates during the adult stage, while overexpression of the let-7 gene causes the early presence of adult cell fate during larval stages [35]. Both lin-4 and let-7 miRNAs are highly conserved; miR-125a and miR-125b are the mammalian orthologues of lin-4 [36,37].
The impact of miRNAs in embryonic development has been demonstrated in different organisms either by dissecting the miRNA pathway or by functional and expression pattern analyses of miRNAs. In mice, different miRNAs are present during all stages of embryonic development. Deletion of Dicer, Dgcr8, or Ago2 induced early post-implantation lethality [38,39,40,41]. Dicer 1 mutant mouse embryos exhibited a 50% lethality rate at the 7.5-day embryonic stage; surviving embryos exhibited morphological abnormalities and suppressed Oct4 and brachyury expression, indicating an embryonic developmental arrest and deficient pluripotency [38]. Homozygous deletion of the first and second exons of the Dicer gene resulted in severe hypomorphic embryos with retarded phenotype and mid-gestation death, suggesting an essential role for Dicer in normal mouse embryonic development [42]. Moreover, Dgcr8 knockout mouse embryos died early in development and displayed extreme morphological defects [41].
miRNA profiling uncovered developmental stage-specific miRNA expression. Zygotes inherit both maternal and paternal miRNAs [43,44]; however, the maternal miRNA pool is largely depleted between the one- and two-cell stages. Subsequently, miRNA expression is increased upon the activation of zygotic transcription [43]. Remarkably, certain stem-cell-specific miRNAs, such as miR-290 cluster members, are the first de novo expressed miRNAs in early embryogenesis [43,45,46]. Similarly, in rabbits, the expression of ocu-miR-290 cluster members begins at early embryonic stages [47]. Furthermore, ocu-miR-512-5p, which is evolutionarily related to miR-290 and its human homolog miR-371, is also expressed in early stages of rabbit embryonic development [47]. miR-29b is another important development regulator. It is highly expressed in the two-cell-stage mouse embryos and downregulated in the four-cell stage. Inhibition of miR-29b led to early developmental blockade by downregulating Dnmt3a/b and disrupting DNA methylation [48]. The placenta-specific C19MC miRNAs play significant roles in the fate of trophoblasts. For example, miR-519d regulates human trophoblast migration [49]. Additionally, a high expression of ocu-miR-512-5p, another C19MC family member, was reported in rabbit trophoblasts and hypoblasts, in line with its importance in pre-implantation [47]. Likewise, hsa-miR-512-3p miRNAs are among the most highly expressed miRNAs in human blastocysts [50]. miR-376c (member of the hsa-miR-379/miR-656 cluster) promotes cell proliferation and invasion of human trophoblast cells [51], whereas miR-155 inhibits their cell proliferation and migration [52]. The miR-302 cluster is a highly expressed stem-cell-specific miRNA cluster in rabbit pre-implantation embryos [47]. Similar to rabbits, miR-302 cluster members are highly expressed in the human blastocysts [50]. miR-21 is expressed in both human and mouse oocytes and blastocysts [53,54]. It is associated with oocyte maturation, blastocyst formation, and pre-implantation embryonic development [54]. The let-7 family also plays a crucial role in mammalian embryonic development. The expression of let-7 in mouse embryos regulates inner cell mass cell fate determination and reinforces blastocyst formation [55].

4. Discovery of miRNA Clusters in Stem Cells

To date, many studies have demonstrated the regulatory function of miRNAs (both canonical and non-canonical) in the self-renewal and differentiation of ESCs and iPSCs. Many canonical miRNAs, such as miR-302 and miR-290 clusters, reportedly promote ESC properties. miR-320 and miR-702 are the two first-discovered non-canonical miRNAs expressed in mouse ESCs [56]. Interestingly, miR-133a regulates the transcription of the DNMT3B gene in human ESCs through a non-canonical pathway when it is translocated to the nucleus, while it regulates skeletal and cardiac muscle function via canonical target mRNA repression in the cytoplasm [57].
DICER deletion has induced a proliferation defect, hindered teratoma and chimera formation, and constrained the differentiation of mESCs [58,59] and hESCs [60]. Similarly, Dgcr8-knockout mESCs proliferate slowly and exhibit either delayed or reduced differentiation potential, accompanied by defects in embryonic anatomy and teratoma formation [41,61]. While Dicer- and Dgcr8-mutant ESCs contributed to an overall analysis of miRNA functional aspects in ESC properties, cloning and deep sequencing of non-coding small RNAs from stem cells led to the discovery and profiling of stem-cell-specific miRNAs with potential functions in the self-renewal and differentiation of ESCs. ESC-associated transcription factors, including OCT4, NANOG, SOX2, and REX1, regulate ES-specific miRNAs through binding to their promoter region [62,63]. As a prominent example, the miR-290/295 cluster was identified as a stem-cell-specific miRNA cluster in mice by cloning and deep sequencing [64]. Subsequently, the human homolog clusters miR-302/367 and miR-371/373 were also identified by cDNA cloning in human ESCs [65]. Additionally, the deep sequencing of small RNAs showed that the rabbit ES-like cells highly express the ocu-miR-302/367 cluster, which potentially maintains pluripotency by negatively modulating Lefty [47].

4.1. miRNA Clusters Regulate Pluripotency

miR-302/367, miR-290/295, and their human homolog, the hsa-miR-371/373 cluster, are highly expressed in vertebrate ESCs. They modulate self-renewal and pluripotency through regulating cell cycle progression. These clusters are downstream targets of ESC-specific transcription factors, including OCT4, SOX2, and NANOG, which are essential for the self-renewal and maintenance of pluripotency in ESCs [47,63,66,67,68]. In both mouse and human ESCs, OCT4 and SOX2 bind to conserved promoter regions of miR-302 and activate its transcription. Furthermore, miR-302 directly suppresses differentiation marker genes, resulting in the high-level expression of pluripotent-related transcription factors, such as OCT4 [69]. miR-195 and miR-372a are also highly expressed in hESCs and maintain the proliferative capacity and self-renewal of hESCs through negative cell cycle modulators [70].

4.2. miRNA Clusters Are Involved in Stem Cell Differentiation

miRNAs are also involved in the initiation of stem cell differentiation by suppressing pluripotency-associated pathways. In human ESCs, post-transcriptional repression of OCT4, SOX2, and KLF4 mediated by miR-145 leads to the suppression of self-renewal, and consequently the induction of differentiation [71]. Likewise, miR-134, miR-296, and miR-470 promote the differentiation of mouse ESCs by suppressing Nanog, Oct4, and Sox2 [72,73]. miR-1305 induces the differentiation of human ESCs through the repression of POLR3G, which is an activator of the OCT4/NANOG pathway [74,75]. Other differentiation associated-miRNAs in mice are miR-34a, miR-100, and miR-137, which activate differentiation marker genes via the regulation of epigenetic mediators through targeting Sirt1, Smarca5, and Jarid1b mRNAs, respectively [76]. Furthermore, miR-27a and miR-24 silence self-renewal and promote differentiation by downregulating pluripotent-specific transcription factors and signal transducers of mESC self-renewal networks. The downregulation of Oct4 and Foxo1 and further suppression of signaling pathways through direct targeting of the LIF receptor gp130 and the two important signal transducers Smad3 and Smad4 result in decreased expression of c-Myc, hence creating a mutual negative feedback loop to upregulate the expression of the miRNAs to maintain the differentiated state [77]. The let-7 miRNA family members also regulate the transition from self-renewing stem cells to differentiated cell types in both human and mouse ESCs. Contrary to the abovementioned pluripotent-specific miRNAs, let-7 miRNAs suppress the self-renewal of ESCs through cell cycle progression [78,79,80].
It is important to note that miRNAs might have context-dependent functions and can vary across different organisms and cell types. Numerous miRNAs contribute to the maintenance of early embryonic development and embryonic stem cell properties. In the following section, we highlight the well-studied stem-cell-specific miRNA clusters and compare their expression profiles and functions in humans, mice, rabbits, and chickens.

5. Major miRNA Clusters of ESCs

5.1. miR-302/367 Cluster

5.1.1. Characteristics of Cluster

The polycistronic human miR-302/367 cluster is located in the intron of the LARP7 gene at the 4q25 region and consists of ten miRNAs: miR-302a-3p, miR-302a-5p, miR-302b-3p, miR-302b-5p, miR-302c-3p, miR-302c-5p, miR-302d-3p, miR-302d-5p, miR-367-3p, and miR-367-5p [64,65,81]. All 3′ mature miRNAs share the same seed sequence of 5′-AAGTGC-3′, except for miR-367 which harbors a slightly different seed sequence; however, they all have common mRNA targets [68,82]. The cluster is well conserved among the vertebrates (Figure 1). As it is shown in Figure 1, several species exhibit a common cluster structure, comprising four miR-302s (a–b) and one miR-367. Interestingly, the Aves class expresses an extra miRNA within the miR-302/367 cluster, such as gga-miR-1811 in chickens, which shares a highly similar seed sequence with miR-367, suggesting that it might be generated by the tandem duplication of miR-367 [81].
The miR-302/367 cluster’s promoter itself is a highly conserved region among vertebrates [47,83]. The cluster’s expression is regulated by ESC-specific transcription factors (OCT3/4, SOX2, KLF4, MYC, and NANOG) in mice and humans [68,84].

5.1.2. miR-302/367 Expression in Mice, Humans, and Rabbits

In addition to cell cycle regulation, miR-302 cluster members modulate the self-renewal-related genes by repressing epithelial–mesenchymal transition and apoptotic pathways [85]. The miR-302/367 cluster is predominantly expressed in human ESCs, mouse epiblast stem cells (EpiSCs), and rabbit ES-like cells, whereas its expression in mouse ESCs is slightly lower [47,65,86]. In addition, it is highly expressed in human iPSCs and downregulated upon differentiation [87]. Overexpression of the miR-302/367 cluster in both mouse and human somatic cells results in cellular reprogramming the iPSC state and preserves the stemness properties of ESCs [88,89].
In rabbits, miR-302 expression begins at 3.5 dpc of pre-implanted embryos, whereas mouse embryos express miR-302 starting from day 6.5 dpc. The miR-302 cluster reaches the highest expression at the 6 dpc stage in rabbit embryos, and at 7.5 dpc in mouse embryos; its expression is rapidly downregulated by 8.5 dpc in mice [47,68].

5.1.3. Gga-miR-302b-3p/5p Expression in Chicken Embryos and PGCs

Most chicken stem-cell-specific miRNAs are conserved with other vertebrate model species [90]. Gga-miR-302a is highly expressed in the chicken blastoderm and regulates the undifferentiated state of blastodermal cells and primordial germ cells (PGCs) by silencing Sox11, a somatic transcription factor [91]. It has also been reported that gga-miR-302b regulates glucose phosphate isomerase (GPI) expression; therefore, it modulates chicken PGC proliferation [92]. A recent study based on an inhibition assay demonstrated that gga-miR-302b (both -3p and -5p miRNAs) promotes the proliferation of PGCs and decreases apoptosis. In addition, the dual inhibition of -3p and -5p miR-302b caused an excessive increase in the number of apoptotic cells [93].

5.1.4. Targets of miR-302/367 Cluster

To achieve the functional characterization of miRNAs, it is crucial to identify their target genes. Cell cycle regulators were the first-identified miR-302/367 targets both in human and mouse ESCs. In human ESCs, miR-302 modulates G1/S transition by directly targeting components of the cell cycle pathway, such as CYCLIN D1 and D2, cyclin-dependent kinase 2 (CDK2), CDK4, RB, E2F1, P130, and CDK6 [68]. In addition to repressing CYCLIN D1/D2 and other cell cycle components, it promotes S phase entry through an alternative pathway [94]. Likewise, in mouse ESCs, miR-302/367 suppresses the cyclin-dependent kinase inhibitor 1, also known as p21, thus inducing the G1 to S phase transition and cell proliferation [61]. It is also suggested that miR-302a modulates cell cycle progression in mouse ESCs through the negative regulation of Lats2, a tumor suppressor gene [95]. Sodium butyrate-mediated upregulation of the miR-302/367 cluster preserves the expression of key cell cycle regulators and supports self-renewal of human ESCs [96]. On the other hand, it also downregulates BNIP3L/Nix, thus inhibiting spontaneous apoptosis in hESCs [97]. LEFTY1 and LEFTY2 (Nodal inhibitors) are other prominent targets of miR-302 members. Post-transcriptional downregulation of LEFTY by miR-302 inhibits the expression of TGFβ/Activin/ NODAL family proteins and retains the pluripotency of hESCs through activating SMAD2/3 and inducing NANOG expression [98,99,100]. Similarly, Lefty has been identified as a direct target of miR-302 in rabbit ES-like cells by the transient inhibition of ocu-miR-302a [47]. SMAD7 is a direct target of miR-367 in human pancreatic cancer cells and it promotes the invasion and metastasis of pancreatic cancer cells through the TGF-β signaling pathway [101]. miR-302/367 also promotes BMP signaling through direct targeting of BMP inhibitors, including TOB2, DAZAP2, and SLAIN1, thus maintaining pluripotency by repressing neural differentiation [102,103].
In addition to cell cycle and signaling pathway regulation, the miR-302 cluster modulates multiple key epigenetic regulators in somatic cells, including the lysine-specific histone demethylase enzymes AOF1 and AOF2 (also called KDM1B and KDM1A, respectively) and the methyl-CpG binding proteins MECP1 and MECP2. Post-transcriptional suppression of these epigenetic regulators by miR-302 members induces global DNA demethylation and promotes reprogramming and iPS cell establishment [104]. Furthermore, MBD2 (methyl-DNA binding domain protein 2) is a direct target of miR-302 to accomplish complete reprogramming of the iPS cell [105]. The main targets of miR-302/367 clusters are schematically presented in Figure 2.

5.2. C19miRNA Cluster

5.2.1. Characteristics of C19M Cluster

C19MC (chromosome 19 miRNA cluster), one of the longest miRNA gene clusters in the human genome, is located on chromosome 19 and extends for about 100 kb. The cluster contains 46 highly homologous pre-miRNA genes, producing 56 mature miRNAs. Despite the high similarity of miRNAs in the cluster, they harbor 16 distinct seed sequences [106]. The cluster itself exhibits a unique genomic structure: most miRNA genes are flanked by ~400–700 bp Alu repeated sequences and short exons with highly repetitive DNA elements [107,108]. The Alu element reportedly mediates gene duplication events in this region, resulting in the expansive miRNA cluster and allowing for its high expression from the multiple copies [107,109]. Reciprocally, free Alu transcripts are post-transcriptionally suppressed by expressed miRNAs from the cluster; thus, the genome self-destruction caused by high rates of duplicative Alu transposition can be prevented [107]. In addition, hsa-miR-371/373 is located in close proximity to C19MC at about 20 kbp downstream of the cluster.
It has been suggested that C19MC miRNAs are primate-specific and have no orthologous regions in the mouse genome; however, we have previously identified three homologs in rabbits, including ocu-miR-512, ocu-miR-498, and ocu-miR-520e [47]. All three mature rabbit miRNAs presented high sequence similarity to their human homologs. They are located 5′ to the rabbit miR-290/295 cluster on the reverse strand of the pseudo-chromosome chrUn0226 in the same order as in humans (Figure 3a,b). Ocu-miR-520e shares the common consensus seed sequence of “AAGTGCT” with its human homologs, but ocu-miR-512 harbors a slightly different seed sequence.

5.2.2. Expression of Human C19MC Cluster and Its Rabbit Homologs

The C19MC cluster miRNAs are trophoblast-specific and are highly expressed in the placenta [108]. In humans, C19MC is exclusively expressed from the paternal chromosome driven by an upstream promoter region. Mono-allelic expression of the C19MC cluster was demonstrated to be regulated through the DNA demethylation of the CpG-rich promoter region. Transcription of the C19MC cluster results in a primary transcript harboring the entire C19MC gene cluster, which is further processed into precursor miRNA and subsequently generates mature miRNAs via the Dgcr8-Drosha complex [110]. A recent study demonstrated that the pri-miRNA maturation of C19CM is tissue-specific and enhancer-mediated. A strong association of Drosha with the promoter/enhancer regions in human results is necessary for the efficient pri-miRNA maturation and to achieve a high expression level in placenta cells compared to the stem cells [111].
C19MC miRNAs are present in primary human-trophoblast-derived vesicles, particularly in the villous trophoblasts (VTs) [49,112]. They have also been detected in human extravillous trophoblasts (EVTs), where they may regulate migration [49]. Among C19MC-related miRNAs, ocu-miR-512 showed a high expression level in trophoblasts and hypoblasts of rabbit pre-implanted embryos [47].
In addition to the placenta, C19MC miRNAs are expressed in human ESCs and contribute to stemness [113,114]. Almost all C19MC miRNAs are active in naïve human ESCs, display high expression levels, and are epigenetically silenced in primed hESCs [115]. Unlike hESCs, rabbit ES-like cells do not exhibit a significant expression level of C19MC, which may reflect the primed state of rabbit ES-like cells [47]. The cluster is also expressed in human iPSCs and enhances reprogramming by suppressing epithelial-to-mesenchymal transition [116,117].
Furthermore, C19MC miRNAs are selectively expressed in various cancer types, such as breast cancer, hepatocellular carcinoma, embryonal brain tumors, infantile hemangioma, testicular germ cell tumors, parathyroid tumors, and thyroid adenomas. The overexpression of cancer-derived, circulating C19MC miRNAs, which commonly correspond to tumor size and proliferative state, makes them attractive potential biomarkers for diagnosis and treatment response monitoring [118,119,120,121,122,123,124,125].

5.2.3. Targets of C19MC Cluster

Computational miRNA target prediction tools identified 4734 target genes for the C19MC cluster [114,115]. Among them, genes involved in chromatin structure modifications [114], the p53 pathway (including CCNG2, CDKN1A, PMAIP1, TP53INP1, and ZMAT3), and the extracellular matrix (ECM) [115] were enriched in hESCs.
miR-524 enhances somatic cell reprogramming by targeting TP53INP1 (Tumor Protein P53 Inducible Nuclear Protein 1), promotes cell proliferation, and inhibits apoptosis [116]. Moreover, miR-524 downregulates ZEB2 and SMAD4 (epithelial–mesenchymal-transition-related genes) and promotes mesenchymal-to-epithelial transition, which is required for the initiation of reprogramming [126,127].

5.3. Mmu-miR-290/295, hsa-miR-371/373, and ocu-miR-290/295 Clusters

5.3.1. Cluster Characteristics

The mmu-miR-290/295, hsa-miR-371/373, and ocu-miR-290/295 clusters are highly conserved in humans, mice, rabbits, chimpanzees, rats, dogs, and cows [128,129]; however, some differences are present in their structure, number of members, and genomic location.
The mmu-miR-290/295 cluster, which is the most abundant miRNA cluster in mouse ESCs [130], is coded by a 2.2 kb region located on chromosome 7 (Figure 4a). The single spliced primary transcript is processed into 14 mature miRNAs: miR-290-5p, miR-290-3p, miR-291a-5p, miR-291a-3p, miR-291b-5p, miR-291b-3p, miR-292-5p, miR-292-3p, miR-293-5p, miR-293-3p, miR-294-5p, miR-294-3p, miR-29-5p, and miR-295-3p [64,128]. All pre-miRNAs of the cluster share the same “AAGTGC” seed sequence, except for the miR-293 pre-miRNA (Figure 4b). The cluster’s transcription is regulated by a 332 nt intragenic enhancer region within the cluster [131]. Additionally, pluripotency-associated transcription factors, such as Oct4, Sox2, Snai, c-Myc, and Nanog, directly control the cluster expression by binding an upstream promoter element [66,132].
miR-371/373, a human ortholog of the mmu-miR-290/295 cluster, is located in close proximity to C19MC on chromosome 19 (Figure 4a) [64,125]. The hsa-miR-371/373 cluster is transcribed into four pre-miRNAs, pre-miR-371a, pre-miR-371b, pre-miR-372, and pre-miR-373, and further processed into six mature mRNAs: miR-371a-3p, miR-371a-5p, miR-371b-3p, miR-371b-5p, miR-372, and miR-373 [65,133,134]. The ESC-specific seed sequence “AAGTGC” can be found in all of the cluster’s miRNAs (Figure 4b).
Rabbit homologs of the mmu-miR-290/295 cluster are located on the reverse strand of a short pseudo-chromosome (chrUn0226) and are comprised of three mature miRNAs: ocu-miR290-5p, ocu-miR-292-3p, and ocu-miR-294-3p (Figure 4a). The ocu-miR-294-3p miRNA has also been mapped on chromosome 2 of the rabbit genome. Like hsa-miR-371/373, the ocu-miR290/295 cluster is located 3′ to the rabbit C19MC (Figure 4a). Interestingly, based on putative secondary structure prediction, ocu-miR-290-5p and ocu-miR-292-3p form a single pre-miRNA. Only ocu-miR-294 contains the stem-cell-specific seed sequence “AAGTGCT” (Figure 4b) [47].

5.3.2. Evolution of mmu-miR-290/295, hsa-miR-371/373, and ocu-miR-290/295 Clusters

It is speculated that clustered miRNAs evolved via gene duplication, genomic rearrangements, and specific gene repressions. Evolving novel clusters might have comprised highly homologous miRNAs or could be joined with other miRNA families. In addition, miRNA family members can either be located in a cluster family or distributed randomly throughout the genome [135,136,137].
A cluster sequence and repeat analysis showed a close evolutionary relationship between human, mouse, and rabbit miRNA clusters. The miR-290/295 cluster has likely evolved from miR-290 or miR-291a and appears to be the evolutionary precursor. The individual pre-miRNA hairpin sequences of mmu-miR-290/295 and hsa-miR-371/373 clusters are homologous to each other. It appears that mouse miR-290/295 is the possible origin of the human miR-371/373 cluster, while the hsa-miR-371/373 cluster itself gave rise to another miRNA cluster, the hsa-miR-512 cluster, located in close proximity to its ancestor on human chromosome 19 [67]. Moreover, the enthalpy levels of pre-miR-372 and pre-miR-373 are similar to mmu-miR-291a, mmu-miR-291b, and mmu-miR-294 [67]. It has also been demonstrated that hsa-miR-373 is a member of the miR-520/373 family, composed of the hsa-miR-302/367, hsa-miR-371/373, and hsa-miR-520 clusters that share identical seed sequences [138,139,140].
Furthermore, according to the seed sequence and target interaction analysis, it seems that mmu-miR-290/295 and hsa-miR-371/373 share the same seed repertoire, given that in mice the cluster transcribes seven pre-miRNAs and in humans the cluster transcribes just three pre-miRNAs but the pre-miR-371 carries all the seeds to form the orthologs pre-miR-290, pre-miR-292, and pre-miR-293 in mice [141].
As mentioned above, the rabbit miR-290/295 cluster resides in only three miRNA members, representing a low evolutionary conservation with its homolog cluster in mice. Moreover, ocu-miR-290-5p and ocu-miR-292-3p form a single pre-miRNA, in contrast to the mouse homolog cluster which encodes three pre-miRNAs (pre-miR-290, pre-miR-291a, and pre-miR-292) in the same genomic region [47]. In addition, in proximity to the ocu-miR-290/295 cluster on the contig chromosome, there are three miRNAs of the C19MC cluster of ocu-miR-512, ocu-miR-520e, and ocu-miR-498, similar to the human and mouse cluster distribution. Hence, it is possible that these rabbit miRNAs located on the contig chromosome might recapitulate the evolution of human homologs and derive from the same ancestor by a duplication event [47].

5.3.3. The Expression of mmu-miR-290/295, hsa-miR-371/373, and ocu-miR-290/295 Clusters

Mmu-miR-290/295 miRNAs are the first de novo expressed miRNAs in mouse embryos, starting at the two- to four-cell stage and exhibiting high expression in blastocysts [43,45,46]. The cluster is abundantly expressed in undifferentiated mESCs and maintains the pluripotent state of mESCs [66,130]. The overexpression of mmu-miR290/295 miRNAs under serum starvation retains the stem cell properties of mESCs and regulates the cell cycle by preventing a G1 stop and extending the survival of the stem cell population [67]. In addition, the simultaneous introduction of mmu-miR-290/295 along with Oct4, Sox2, and Klf4 (OSK) enhances the reprogramming of mouse embryonic fibroblasts into mouse iPSCs [142].
In contrast to mmu-miR-290/295, hsa-miR-371/373 expression in human ESCs is considerably lower and comprises only 1% of the total miRNA pool in hESCs [65,143]. Hsa-miR-372 and hsa-miR-373 display a high level of expression in human testicular germ cell tumors, indicating their oncogenic potential [133]. The introduction of hsa-miR-372 along with hsa-miR-302b enhanced the reprogramming efficiency of human fibroblasts [144].
The ocu-miR-290/295 miRNAs show low expression levels in rabbit ES-like cells, whereas they are highly expressed during preimplantation embryonic development, implying their potential role during early embryonic development [47].
Taken all together, the expression patterns of mmu- and ocu-miR-290/295 and hsa-miR-371/373 in ESCs and in early embryos suggest a prominent function in early embryonic development.

5.3.4. miR-290/295 Cluster Targets

The mmu-miR-290/295 cluster is a well-described cell cycle regulator miRNA cluster. A short G1 phase and lack of a G1/S checkpoint are characteristics of the ESC cell cycle. The mouse miR-290/295 cluster regulates G1/S transition through the downregulation of cell cycle inhibitors such as p21, Lats2, Wee1, and Fbxl5, thus maintaining the pluripotent state of mouse ESCs [56,61,67,145]. Additionally, rapid G1/S transition promoted by mmu-miR-294 miRNA is Retinoblastoma gene (Rb)-independent. The accumulation of cells in G1 is regulated by direct targeting of the Rb family under nutrient starvation [94]. On the other hand, the mmu-miR-290/295 cluster reportedly represses S/G2 transition through p53 and Cyclin D1 [67,146]. Therefore, the mmu-miR-290/295 cluster contributes to pluripotency by accelerating G1 and extending the S phase in mESC.
Furthermore, mmu-miR-290/295 modulates DNA methylation in the pre-implantation embryos by the targeting of retinoblastoma-like 2 (Rbl2) and the subsequent inhibition of Dnmt3b [62,147]. On the one hand, pluripotent-associated transcription factors such as Oct4, Sox2, and Nanog either directly or indirectly regulate the transcription of DNMT3B. On the other hand, the core promoter region of the mmu-miR-290/295 cluster is a direct target for pluripotent-associated transcription factors. Altogether, pluripotent-associated transcription factors, the mmu-miR-290/295 cluster, Rbl2, and Dnmt3b build a regulatory network that regulates DNA methylation in early embryonic development and in ESCs [148]. Moreover, mmu-miR-290/295 directly targets Dkk-1, which is a Wnt pathway inhibitor, resulting in the upregulation of c-Myc, a downstream target of the Wnt signaling pathway [149,150]. Thus, mmu-miR-290/295 miRNAs partially favor pluripotency upon differentiation.
The mmu-miR-290/295 cluster together with miR-302/376 promote transition from naïve to primed pluripotency by enhancing the activity of the MEK pathway through the direct repression of Akt1 [151]. In addition, mmu-miR-290/295 miRNAs are required for the incorporation of two core components of polycomb repressive complexes 2 (Prc2), Ezh2, and Suz12 into promoters of bivalent differentiation genes in order to maintain the pluripotent state of mouse ESCs [152,153].
The mmu-miR-290/295 cluster also enhances the reprogramming of somatic cells and the quality of mouse iPSCs [89,142]. Mmu-miR-291 post-transcriptionally suppresses the methyltransferase Ash1l expression and consequently downregulates HOX genes, which in turn promote reprogramming through polycomb-mediated gene silencing [153].
In summary, the mmu-miR-290/295 cluster modulates both stemness and differentiation characteristics of mouse ESCs and embryos by regulating the cell cycle, de novo DNA methylation, apoptosis, and the transcription of pluripotent-associated transcription factors (Figure 5). To date, no target gene has been predicted for the rabbit miR-290/295 cluster. Certainly, target recognition and the investigation of functional characteristics are indispensable to discovering and describing the impact of the ocu-miR-290/295 cluster in early embryonic development and stem cell biology.

5.3.5. Targets of hsa-miR-371/373 Cluster

To date, very little known is about how the hsa-miR-371-373 cluster can integrate into the pluripotency regulation of stem cells. The miR-372 miRNA together with miR-195 can partially rescue DICER knockdown phenotypes in hESCS but this is not sufficient to influence the cell cycle kinetics in wild-type hESCs. However, miR-372 represses P21 (a CDK inhibitor); thus, it indirectly controls the G1/S transition and consequently regulates hESC division [70].
Due to its high level of expression and its potential biomarker capacity in different human tumor cells, its mechanism of action has been further dissected in relation to its oncogenic function. The miR-371/373 cluster activates WNT/β-catenin signaling through the repression of DKK1, which in turn induces cell growth and the invasive activity of tumor cells in humans [154]. However, it is not determined if the miR-371-373 cluster preserves the pluripotency of hESCs by activation of the WNT/β-catenin signaling pathway. In testicular germ cell tumor cells, the suppression of LATS2 by miR-371/373 miRNAs prevents p53-mediated CDK inhibition and promotes tumorigenic growth [133]. Moreover, miR-373 miRNA represses CD44, thus leading to tumor migration and invasion in human breast cancer [138].
It also has been reported that miR-371/373 regulates glycolysis through the repression of MBD2I, resulting in promoting the expression of MYC and thus increasing human fibroblast reprogramming [155].

6. Conclusions

miRNAs are well-recognized, major post-transcriptional regulators of most cellular events including proliferation, cell cycle progression, differentiation, survival, and apoptosis in many cell types. Extensive research on the regulatory function of miRNAs indicates that miRNAs play crucial roles in stem cell properties. Pluripotent stem cells have enormous potential in the field of regenerative medicine, disease modeling, and new drug discoveries. In this review, we aimed to compare and discuss the regulatory functions of stem-cell-specific miRNA clusters and their action on the maintenance and regulation of ESC biology in vertebrates. We also discussed the expression profile of stem-cell-specific miRNAs in early embryogenesis, which may play an important role in the establishment and maintenance of pluripotent progenitor cells. Furthermore, we compared the stem-cell-specific human miRNAs with our other vertebrate model species.
Several miRNA clusters have been identified to regulate the stemness and pluripotency of stem cells. The most important miRNA clusters which are highly expressed in ESCs of vertebrates are miR-302/367 and miR-290/295 and its human homologue miR-371/373. They regulate the self-renewal and pluripotency of ESCs through the modulation of cell cycle progression. These miRNA clusters share a highly conserved seed sequence, “AAGUGCU” (referred to as stem-cell-specific miRNA) (Figure 2 and Figure 4), and induce the pluripotency of ESCs by direct targeting of the 3′ UTR of key ESC transcription factors, such as OCT4, SOX2, and NANOG. They also play a predominant role in vertebrate early development. Likewise, C19MC miRNAs are highly expressed in human ESCs, contribute to the stemness state of hESCs, and prevent their differentiation. Some members of C19MC miRNAs and their rabbit homologs also share the same stem-cell-specific “AAGTGCT” seed sequence (Figure 3).
The profiles of ESC-specific miRNA clusters and their relative functions in vertebrates which have been discussed through this review are summarized in Table 1.
This review gives outstanding insights into the cell cycle regulation of stem cells by miRNAs. A deep understanding of regulatory molecular networks in which miRNAs are interacting will greatly enhance our knowledge of miRNAs’ contribution to stem cell biology and therefore open promising avenues toward stem cell therapy.

Author Contributions

Conceptualization: E.G., P.M. and M.T.S.A.; writing—original draft preparation: P.M., M.T.S.A. and E.G.; writing—review and editing: B.L., A.E. and R.T.; visualization: M.T.S.A. and N.T.S.; supervision: E.G.; funding acquisition: E.G. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by National Research, Development and Innovation Office, grants RRF-2.3.1-21-2022-00007 and 2019-2.1.11-TÉT-2019-00036.

Institutional Review Board Statement

All applied methods in NBGK-HGI were approved by the Directorate of Food Safety and Animal Health of the Government Office of Pest County (License number: PE/EA197-4/2016) and by the Institutional Ethical Review Board.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are available on request from the corresponding author.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Lee, C.T.; Risom, T.; Strauss, W.M. MicroRNAs in mammalian development. Birth Defects Res. C Embryo Today 2006, 78, 129–139. [Google Scholar] [CrossRef] [PubMed]
  2. Rosa, A.; Brivanlou, A.H. MicroRNAs in early vertebrate development. Cell Cycle 2009, 8, 3513–3520. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Bartel, D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004, 116, 281–297. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Bartel, D.P. MicroRNAs: Target recognition and regulatory functions. Cell 2009, 136, 215–233. [Google Scholar] [CrossRef] [Green Version]
  5. Lee, Y.; Kim, M.; Han, J.; Yeom, K.H.; Lee, S.; Baek, S.H.; Kim, V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004, 23, 4051–4060. [Google Scholar] [CrossRef] [Green Version]
  6. Ha, M.; Kim, V.N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 2014, 15, 509–524. [Google Scholar] [CrossRef]
  7. Franca, G.S.; Vibranovski, M.D.; Galante, P.A. Host gene constraints and genomic context impact the expression and evolution of human microRNAs. Nat. Commun. 2016, 7, 11438. [Google Scholar] [CrossRef] [Green Version]
  8. Kim, Y.K.; Kim, V.N. Processing of intronic microRNAs. EMBO J. 2007, 26, 775–783. [Google Scholar] [CrossRef] [Green Version]
  9. Georgakilas, G.; Vlachos, I.S.; Paraskevopoulou, M.D.; Yang, P.; Zhang, Y.; Economides, A.N.; Hatzigeorgiou, A.G. microTSS: Accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat. Commun. 2014, 5, 5700. [Google Scholar] [CrossRef] [Green Version]
  10. Guo, L.; Zhao, Y.; Zhang, H.; Yang, S.; Chen, F. Integrated evolutionary analysis of human miRNA gene clusters and families implicates evolutionary relationships. Gene 2014, 534, 24–32. [Google Scholar] [CrossRef]
  11. Pal, A.S.; Kasinski, A.L. Animal Models to Study MicroRNA Function. Adv. Cancer Res. 2017, 135, 53–118. [Google Scholar] [CrossRef] [Green Version]
  12. Baskerville, S.; Bartel, D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11, 241–247. [Google Scholar] [CrossRef] [Green Version]
  13. Lagos-Quintana, M.; Rauhut, R.; Lendeckel, W.; Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294, 853–858. [Google Scholar] [CrossRef] [Green Version]
  14. Seitz, H.; Royo, H.; Bortolin, M.L.; Lin, S.P.; Ferguson-Smith, A.C.; Cavaille, J. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res. 2004, 14, 1741–1748. [Google Scholar] [CrossRef] [Green Version]
  15. Yeom, K.H.; Lee, Y.; Han, J.; Suh, M.R.; Kim, V.N. Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res. 2006, 34, 4622–4629. [Google Scholar] [CrossRef] [Green Version]
  16. Yi, R.; Qin, Y.; Macara, I.G.; Cullen, B.R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes. Dev. 2003, 17, 3011–3016. [Google Scholar] [CrossRef] [Green Version]
  17. Hutvagner, G.; Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297, 2056–2060. [Google Scholar] [CrossRef] [Green Version]
  18. Chendrimada, T.P.; Gregory, R.I.; Kumaraswamy, E.; Norman, J.; Cooch, N.; Nishikura, K.; Shiekhattar, R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005, 436, 740–744. [Google Scholar] [CrossRef] [Green Version]
  19. Medley, J.C.; Panzade, G.; Zinovyeva, A.Y. microRNA strand selection: Unwinding the rules. Wiley Interdiscip. Rev. RNA 2021, 12, e1627. [Google Scholar] [CrossRef]
  20. Brennecke, J.; Stark, A.; Russell, R.B.; Cohen, S.M. Principles of microRNA-target recognition. PLoS Biol. 2005, 3, e85. [Google Scholar] [CrossRef] [Green Version]
  21. Davis-Dusenbery, B.N.; Hata, A. Mechanisms of control of microRNA biogenesis. J. Biochem. 2010, 148, 381–392. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Okamura, K.; Hagen, J.W.; Duan, H.; Tyler, D.M.; Lai, E.C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007, 130, 89–100. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Ruby, J.G.; Jan, C.H.; Bartel, D.P. Intronic microRNA precursors that bypass Drosha processing. Nature 2007, 448, 83–86. [Google Scholar] [CrossRef] [Green Version]
  24. Babiarz, J.E.; Ruby, J.G.; Wang, Y.; Bartel, D.P.; Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes. Dev. 2008, 22, 2773–2785. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Ender, C.; Krek, A.; Friedlander, M.R.; Beitzinger, M.; Weinmann, L.; Chen, W.; Pfeffer, S.; Rajewsky, N.; Meister, G. A human snoRNA with microRNA-like functions. Mol. Cell 2008, 32, 519–528. [Google Scholar] [CrossRef]
  26. Saraiya, A.A.; Wang, C.C. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog. 2008, 4, e1000224. [Google Scholar] [CrossRef] [Green Version]
  27. Bogerd, H.P.; Karnowski, H.W.; Cai, X.; Shin, J.; Pohlers, M.; Cullen, B.R. A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol. Cell 2010, 37, 135–142. [Google Scholar] [CrossRef] [Green Version]
  28. Miyoshi, K.; Miyoshi, T.; Hartig, J.V.; Siomi, H.; Siomi, M.C. Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. RNA 2010, 16, 506–515. [Google Scholar] [CrossRef] [Green Version]
  29. Yu, J.; Yang, Z.; Kibukawa, M.; Paddock, M.; Passey, D.A.; Wong, G.K. Minimal introns are not “junk”. Genome Res. 2002, 12, 1185–1189. [Google Scholar] [CrossRef] [Green Version]
  30. Berezikov, E.; Chung, W.J.; Willis, J.; Cuppen, E.; Lai, E.C. Mammalian mirtron genes. Mol. Cell 2007, 28, 328–336. [Google Scholar] [CrossRef] [Green Version]
  31. Yang, J.S.; Maurin, T.; Robine, N.; Rasmussen, K.D.; Jeffrey, K.L.; Chandwani, R.; Papapetrou, E.P.; Sadelain, M.; O’Carroll, D.; Lai, E.C. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc. Natl. Acad. Sci. USA 2010, 107, 15163–15168. [Google Scholar] [CrossRef]
  32. Cheloufi, S.; Dos Santos, C.O.; Chong, M.M.; Hannon, G.J. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010, 465, 584–589. [Google Scholar] [CrossRef] [Green Version]
  33. Weiner, A.M. E Pluribus Unum: 3’ end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs. Mol. Cell 2005, 20, 168–170. [Google Scholar] [CrossRef]
  34. Wightman, B.; Ha, I.; Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75, 855–862. [Google Scholar] [CrossRef]
  35. Reinhart, B.J.; Slack, F.J.; Basson, M.; Pasquinelli, A.E.; Bettinger, J.C.; Rougvie, A.E.; Horvitz, H.R.; Ruvkun, G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403, 901–906. [Google Scholar] [CrossRef]
  36. Pasquinelli, A.E.; Reinhart, B.J.; Slack, F.; Martindale, M.Q.; Kuroda, M.I.; Maller, B.; Hayward, D.C.; Ball, E.E.; Degnan, B.; Muller, P.; et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408, 86–89. [Google Scholar] [CrossRef]
  37. Lagos-Quintana, M.; Rauhut, R.; Yalcin, A.; Meyer, J.; Lendeckel, W.; Tuschl, T. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 2002, 12, 735–739. [Google Scholar] [CrossRef] [Green Version]
  38. Bernstein, E.; Kim, S.Y.; Carmell, M.A.; Murchison, E.P.; Alcorn, H.; Li, M.Z.; Mills, A.A.; Elledge, S.J.; Anderson, K.V.; Hannon, G.J. Dicer is essential for mouse development. Nat. Genet. 2003, 35, 215–217. [Google Scholar] [CrossRef]
  39. Liu, J.; Carmell, M.A.; Rivas, F.V.; Marsden, C.G.; Thomson, J.M.; Song, J.J.; Hammond, S.M.; Joshua-Tor, L.; Hannon, G.J. Argonaute2 is the catalytic engine of mammalian RNAi. Science 2004, 305, 1437–1441. [Google Scholar] [CrossRef] [Green Version]
  40. Murchison, E.P.; Stein, P.; Xuan, Z.; Pan, H.; Zhang, M.Q.; Schultz, R.M.; Hannon, G.J. Critical roles for Dicer in the female germline. Genes. Dev. 2007, 21, 682–693. [Google Scholar] [CrossRef] [Green Version]
  41. Wang, Y.; Medvid, R.; Melton, C.; Jaenisch, R.; Blelloch, R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat. Genet. 2007, 39, 380–385. [Google Scholar] [CrossRef] [PubMed]
  42. Yang, W.J.; Yang, D.D.; Na, S.; Sandusky, G.E.; Zhang, Q.; Zhao, G. Dicer is required for embryonic angiogenesis during mouse development. J. Biol. Chem. 2005, 280, 9330–9335. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  43. Tang, F.; Kaneda, M.; O’Carroll, D.; Hajkova, P.; Barton, S.C.; Sun, Y.A.; Lee, C.; Tarakhovsky, A.; Lao, K.; Surani, M.A. Maternal microRNAs are essential for mouse zygotic development. Genes. Dev. 2007, 21, 644–648. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Liu, W.M.; Pang, R.T.; Chiu, P.C.; Wong, B.P.; Lao, K.; Lee, K.F.; Yeung, W.S. Sperm-borne microRNA-34c is required for the first cleavage division in mouse. Proc. Natl. Acad. Sci. USA 2012, 109, 490–494. [Google Scholar] [CrossRef] [PubMed]
  45. Zeng, F.; Schultz, R.M. RNA transcript profiling during zygotic gene activation in the preimplantation mouse embryo. Dev. Biol. 2005, 283, 40–57. [Google Scholar] [CrossRef] [Green Version]
  46. Svoboda, P.; Flemr, M. The role of miRNAs and endogenous siRNAs in maternal-to-zygotic reprogramming and the establishment of pluripotency. EMBO Rep. 2010, 11, 590–597. [Google Scholar] [CrossRef] [Green Version]
  47. Maraghechi, P.; Hiripi, L.; Toth, G.; Bontovics, B.; Bosze, Z.; Gocza, E. Discovery of pluripotency-associated microRNAs in rabbit preimplantation embryos and embryonic stem-like cells. Reproduction 2013, 145, 421–437. [Google Scholar] [CrossRef] [Green Version]
  48. Zhang, J.; Wang, Y.; Liu, X.; Jiang, S.; Zhao, C.; Shen, R.; Guo, X.; Ling, X.; Liu, C. Expression and potential role of microRNA-29b in mouse early embryo development. Cell Physiol. Biochem. 2015, 35, 1178–1187. [Google Scholar] [CrossRef]
  49. Xie, L.; Mouillet, J.F.; Chu, T.; Parks, W.T.; Sadovsky, E.; Knofler, M.; Sadovsky, Y. C19MC microRNAs regulate the migration of human trophoblasts. Endocrinology 2014, 155, 4975–4985. [Google Scholar] [CrossRef] [Green Version]
  50. Rosenbluth, E.M.; Shelton, D.N.; Sparks, A.E.; Devor, E.; Christenson, L.; Van Voorhis, B.J. MicroRNA expression in the human blastocyst. Fertil. Steril. 2013, 99, 855–861.e853. [Google Scholar] [CrossRef]
  51. Fu, G.; Ye, G.; Nadeem, L.; Ji, L.; Manchanda, T.; Wang, Y.; Zhao, Y.; Qiao, J.; Wang, Y.L.; Lye, S.; et al. MicroRNA-376c impairs transforming growth factor-beta and nodal signaling to promote trophoblast cell proliferation and invasion. Hypertension 2013, 61, 864–872. [Google Scholar] [CrossRef] [Green Version]
  52. Dai, Y.; Qiu, Z.; Diao, Z.; Shen, L.; Xue, P.; Sun, H.; Hu, Y. MicroRNA-155 inhibits proliferation and migration of human extravillous trophoblast derived HTR-8/SVneo cells via down-regulating cyclin D1. Placenta 2012, 33, 824–829. [Google Scholar] [CrossRef]
  53. Assou, S.; Al-edani, T.; Haouzi, D.; Philippe, N.; Lecellier, C.H.; Piquemal, D.; Commes, T.; Ait-Ahmed, O.; Dechaud, H.; Hamamah, S. MicroRNAs: New candidates for the regulation of the human cumulus-oocyte complex. Hum. Reprod. 2013, 28, 3038–3049. [Google Scholar] [CrossRef] [Green Version]
  54. Dehghan, Z.; Mohammadi-Yeganeh, S.; Rezaee, D.; Salehi, M. MicroRNA-21 is involved in oocyte maturation, blastocyst formation, and pre-implantation embryo development. Dev. Biol. 2021, 480, 69–77. [Google Scholar] [CrossRef]
  55. Liu, W.; Chen, J.; Yang, C.; Lee, K.F.; Lee, Y.L.; Chiu, P.C.; Zhang, Y.; Duan, Y.G.; Liu, K.; Yeung, W.S. Expression of microRNA let-7 in cleavage embryos modulates cell fate determination and formation of mouse blastocystsdagger. Biol. Reprod. 2022, 107, 1452–1463. [Google Scholar] [CrossRef]
  56. Kim, V.N. Cell cycle micromanagement in embryonic stem cells. Nat. Genet. 2008, 40, 1391–1392. [Google Scholar] [CrossRef]
  57. Di Mauro, V.; Crasto, S.; Colombo, F.S.; Di Pasquale, E.; Catalucci, D. Wnt signalling mediates miR-133a nuclear re-localization for the transcriptional control of Dnmt3b in cardiac cells. Sci. Rep. 2019, 9, 9320. [Google Scholar] [CrossRef] [Green Version]
  58. Kanellopoulou, C.; Muljo, S.A.; Kung, A.L.; Ganesan, S.; Drapkin, R.; Jenuwein, T.; Livingston, D.M.; Rajewsky, K. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes. Dev. 2005, 19, 489–501. [Google Scholar] [CrossRef] [Green Version]
  59. Murchison, E.P.; Partridge, J.F.; Tam, O.H.; Cheloufi, S.; Hannon, G.J. Characterization of Dicer-deficient murine embryonic stem cells. Proc. Natl. Acad. Sci. USA 2005, 102, 12135–12140. [Google Scholar] [CrossRef]
  60. Teijeiro, V.; Yang, D.; Majumdar, S.; Gonzalez, F.; Rickert, R.W.; Xu, C.; Koche, R.; Verma, N.; Lai, E.C.; Huangfu, D. DICER1 Is Essential for Self-Renewal of Human Embryonic Stem Cells. Stem Cell Rep. 2018, 11, 616–625. [Google Scholar] [CrossRef] [Green Version]
  61. Wang, Y.; Baskerville, S.; Shenoy, A.; Babiarz, J.E.; Baehner, L.; Blelloch, R. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat. Genet. 2008, 40, 1478–1483. [Google Scholar] [CrossRef] [PubMed]
  62. Sinkkonen, L.; Hugenschmidt, T.; Berninger, P.; Gaidatzis, D.; Mohn, F.; Artus-Revel, C.G.; Zavolan, M.; Svoboda, P.; Filipowicz, W. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 2008, 15, 259–267. [Google Scholar] [CrossRef] [PubMed]
  63. Barroso-delJesus, A.; Romero-Lopez, C.; Lucena-Aguilar, G.; Melen, G.J.; Sanchez, L.; Ligero, G.; Berzal-Herranz, A.; Menendez, P. Embryonic stem cell-specific miR302-367 cluster: Human gene structure and functional characterization of its core promoter. Mol. Cell Biol. 2008, 28, 6609–6619. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Houbaviy, H.B.; Murray, M.F.; Sharp, P.A. Embryonic stem cell-specific MicroRNAs. Dev. Cell 2003, 5, 351–358. [Google Scholar] [CrossRef]
  65. Suh, M.R.; Lee, Y.; Kim, J.Y.; Kim, S.K.; Moon, S.H.; Lee, J.Y.; Cha, K.Y.; Chung, H.M.; Yoon, H.S.; Moon, S.Y.; et al. Human embryonic stem cells express a unique set of microRNAs. Dev. Biol. 2004, 270, 488–498. [Google Scholar] [CrossRef] [Green Version]
  66. Marson, A.; Levine, S.S.; Cole, M.F.; Frampton, G.M.; Brambrink, T.; Johnstone, S.; Guenther, M.G.; Johnston, W.K.; Wernig, M.; Newman, J.; et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008, 134, 521–533. [Google Scholar] [CrossRef] [Green Version]
  67. Lichner, Z.; Pall, E.; Kerekes, A.; Pallinger, E.; Maraghechi, P.; Bosze, Z.; Gocza, E. The miR-290-295 cluster promotes pluripotency maintenance by regulating cell cycle phase distribution in mouse embryonic stem cells. Differentiation 2011, 81, 11–24. [Google Scholar] [CrossRef]
  68. Card, D.A.; Hebbar, P.B.; Li, L.; Trotter, K.W.; Komatsu, Y.; Mishina, Y.; Archer, T.K. Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. Mol. Cell Biol. 2008, 28, 6426–6438. [Google Scholar] [CrossRef] [Green Version]
  69. Li, H.L.; Wei, J.F.; Fan, L.Y.; Wang, S.H.; Zhu, L.; Li, T.P.; Lin, G.; Sun, Y.; Sun, Z.J.; Ding, J.; et al. miR-302 regulates pluripotency, teratoma formation and differentiation in stem cells via an AKT1/OCT4-dependent manner. Cell Death Dis. 2016, 7, e2078. [Google Scholar] [CrossRef] [Green Version]
  70. Qi, J.; Yu, J.Y.; Shcherbata, H.R.; Mathieu, J.; Wang, A.J.; Seal, S.; Zhou, W.; Stadler, B.M.; Bourgin, D.; Wang, L.; et al. microRNAs regulate human embryonic stem cell division. Cell Cycle 2009, 8, 3729–3741. [Google Scholar] [CrossRef] [Green Version]
  71. Xu, N.; Papagiannakopoulos, T.; Pan, G.; Thomson, J.A.; Kosik, K.S. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell 2009, 137, 647–658. [Google Scholar] [CrossRef] [Green Version]
  72. Tay, Y.; Zhang, J.; Thomson, A.M.; Lim, B.; Rigoutsos, I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 2008, 455, 1124–1128. [Google Scholar] [CrossRef]
  73. Tay, Y.M.; Tam, W.L.; Ang, Y.S.; Gaughwin, P.M.; Yang, H.; Wang, W.; Liu, R.; George, J.; Ng, H.H.; Perera, R.J.; et al. MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells 2008, 26, 17–29. [Google Scholar] [CrossRef]
  74. Jin, S.; Collin, J.; Zhu, L.; Montaner, D.; Armstrong, L.; Neganova, I.; Lako, M. A Novel Role for miR-1305 in Regulation of Pluripotency-Differentiation Balance, Cell Cycle, and Apoptosis in Human Pluripotent Stem Cells. Stem Cells 2016, 34, 2306–2317. [Google Scholar] [CrossRef]
  75. Wong, R.C.; Pollan, S.; Fong, H.; Ibrahim, A.; Smith, E.L.; Ho, M.; Laslett, A.L.; Donovan, P.J. A novel role for an RNA polymerase III subunit POLR3G in regulating pluripotency in human embryonic stem cells. Stem Cells 2011, 29, 1517–1527. [Google Scholar] [CrossRef]
  76. Tarantino, C.; Paolella, G.; Cozzuto, L.; Minopoli, G.; Pastore, L.; Parisi, S.; Russo, T. miRNA 34a, 100, and 137 modulate differentiation of mouse embryonic stem cells. FASEB J. 2010, 24, 3255–3263. [Google Scholar] [CrossRef]
  77. Ma, Y.; Yao, N.; Liu, G.; Dong, L.; Liu, Y.; Zhang, M.; Wang, F.; Wang, B.; Wei, X.; Dong, H.; et al. Functional screen reveals essential roles of miR-27a/24 in differentiation of embryonic stem cells. EMBO J. 2015, 34, 361–378. [Google Scholar] [CrossRef] [Green Version]
  78. Shim, J.; Nam, J.W. The expression and functional roles of microRNAs in stem cell differentiation. BMB Rep. 2016, 49, 3–10. [Google Scholar] [CrossRef] [Green Version]
  79. Cimadamore, F.; Amador-Arjona, A.; Chen, C.; Huang, C.T.; Terskikh, A.V. SOX2-LIN28/let-7 pathway regulates proliferation and neurogenesis in neural precursors. Proc. Natl. Acad. Sci. USA 2013, 110, E3017–E3026. [Google Scholar] [CrossRef]
  80. Melton, C.; Judson, R.L.; Blelloch, R. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature 2010, 463, 621–626. [Google Scholar] [CrossRef]
  81. Gao, Z.; Zhu, X.; Dou, Y. The miR-302/367 cluster: A comprehensive update on its evolution and functions. Open Biol. 2015, 5, 150138. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  82. Kaid, C.; Silva, P.B.; Cortez, B.A.; Rodini, C.O.; Semedo-Kuriki, P.; Okamoto, O.K. miR-367 promotes proliferation and stem-like traits in medulloblastoma cells. Cancer Sci. 2015, 106, 1188–1195. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  83. Barroso-del Jesus, A.; Lucena-Aguilar, G.; Menendez, P. The miR-302-367 cluster as a potential stemness regulator in ESCs. Cell Cycle 2009, 8, 394–398. [Google Scholar] [CrossRef] [PubMed]
  84. Rahimi, K.; Fuchtbauer, A.C.; Fathi, F.; Mowla, S.J.; Fuchtbauer, E.M. Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host-gene. Sci. Rep. 2021, 11, 11115. [Google Scholar] [CrossRef]
  85. Guo, W.T.; Wang, X.W.; Yan, Y.L.; Li, Y.P.; Yin, X.; Zhang, Q.; Melton, C.; Shenoy, A.; Reyes, N.A.; Oakes, S.A.; et al. Suppression of epithelial-mesenchymal transition and apoptotic pathways by miR-294/302 family synergistically blocks let-7-induced silencing of self-renewal in embryonic stem cells. Cell Death Differ. 2015, 22, 1158–1169. [Google Scholar] [CrossRef] [Green Version]
  86. Jouneau, A.; Ciaudo, C.; Sismeiro, O.; Brochard, V.; Jouneau, L.; Vandormael-Pournin, S.; Coppee, J.Y.; Zhou, Q.; Heard, E.; Antoniewski, C.; et al. Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA 2012, 18, 253–264. [Google Scholar] [CrossRef] [Green Version]
  87. Laurent, L.C. MicroRNAs in embryonic stem cells and early embryonic development. J. Cell Mol. Med. 2008, 12, 2181–2188. [Google Scholar] [CrossRef] [Green Version]
  88. Liao, B.; Bao, X.; Liu, L.; Feng, S.; Zovoilis, A.; Liu, W.; Xue, Y.; Cai, J.; Guo, X.; Qin, B.; et al. MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J. Biol. Chem. 2011, 286, 17359–17364. [Google Scholar] [CrossRef] [Green Version]
  89. Anokye-Danso, F.; Trivedi, C.M.; Juhr, D.; Gupta, M.; Cui, Z.; Tian, Y.; Zhang, Y.; Yang, W.; Gruber, P.J.; Epstein, J.A.; et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell 2011, 8, 376–388. [Google Scholar] [CrossRef] [Green Version]
  90. Shao, P.; Zhou, H.; Xiao, Z.D.; He, J.H.; Huang, M.B.; Chen, Y.Q.; Qu, L.H. Identification of novel chicken microRNAs and analysis of their genomic organization. Gene 2008, 418, 34–40. [Google Scholar] [CrossRef]
  91. Lee, S.I.; Lee, B.R.; Hwang, Y.S.; Lee, H.C.; Rengaraj, D.; Song, G.; Park, T.S.; Han, J.Y. MicroRNA-mediated posttranscriptional regulation is required for maintaining undifferentiated properties of blastoderm and primordial germ cells in chickens. Proc. Natl. Acad. Sci. USA 2011, 108, 10426–10431. [Google Scholar] [CrossRef]
  92. Rengaraj, D.; Park, T.S.; Lee, S.I.; Lee, B.R.; Han, B.K.; Song, G.; Han, J.Y. Regulation of glucose phosphate isomerase by the 3’UTR-specific miRNAs miR-302b and miR-17-5p in chicken primordial germ cells. Biol. Reprod. 2013, 89, 33. [Google Scholar] [CrossRef]
  93. Lazar, B.; Szabadi, N.T.; Anand, M.; Toth, R.; Ecker, A.; Urban, M.; Aponte, M.T.S.; Stepanova, G.; Hegyi, Z.; Homolya, L.; et al. Effect of miR-302b MicroRNA Inhibition on Chicken Primordial Germ Cell Proliferation and Apoptosis Rate. Genes 2021, 13, 82. [Google Scholar] [CrossRef]
  94. Wang, Y.; Melton, C.; Li, Y.P.; Shenoy, A.; Zhang, X.X.; Subramanyam, D.; Blelloch, R. miR-294/miR-302 promotes proliferation, suppresses G1-S restriction point, and inhibits ESC differentiation through separable mechanisms. Cell Rep. 2013, 4, 99–109. [Google Scholar] [CrossRef] [Green Version]
  95. Liang, Y.; Li, Y.; Li, Z.; Liu, Z.; Zhang, Z.; Chang, S.; Wu, J. Mechanism of folate deficiency-induced apoptosis in mouse embryonic stem cells: Cell cycle arrest/apoptosis in G1/G0 mediated by microRNA-302a and tumor suppressor gene Lats2. Int. J. Biochem. Cell Biol. 2012, 44, 1750–1760. [Google Scholar] [CrossRef]
  96. Ware, C.B.; Wang, L.; Mecham, B.H.; Shen, L.; Nelson, A.M.; Bar, M.; Lamba, D.A.; Dauphin, D.S.; Buckingham, B.; Askari, B.; et al. Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell 2009, 4, 359–369. [Google Scholar] [CrossRef] [Green Version]
  97. Zhang, Z.; Hong, Y.; Xiang, D.; Zhu, P.; Wu, E.; Li, W.; Mosenson, J.; Wu, W.S. MicroRNA-302/367 cluster governs hESC self-renewal by dually regulating cell cycle and apoptosis pathways. Stem Cell Rep. 2015, 4, 645–657. [Google Scholar] [CrossRef] [Green Version]
  98. James, D.; Levine, A.J.; Besser, D.; Hemmati-Brivanlou, A. TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells. Development 2005, 132, 1273–1282. [Google Scholar] [CrossRef] [Green Version]
  99. Vallier, L.; Reynolds, D.; Pedersen, R.A. Nodal inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway. Dev. Biol. 2004, 275, 403–421. [Google Scholar] [CrossRef] [Green Version]
  100. Ramos-Mejia, V.; Melen, G.J.; Sanchez, L.; Gutierrez-Aranda, I.; Ligero, G.; Cortes, J.L.; Real, P.J.; Bueno, C.; Menendez, P. Nodal/Activin signaling predicts human pluripotent stem cell lines prone to differentiate toward the hematopoietic lineage. Mol. Ther. 2010, 18, 2173–2181. [Google Scholar] [CrossRef] [Green Version]
  101. Zhu, Z.; Xu, Y.; Zhao, J.; Liu, Q.; Feng, W.; Fan, J.; Wang, P. miR-367 promotes epithelial-to-mesenchymal transition and invasion of pancreatic ductal adenocarcinoma cells by targeting the Smad7-TGF-beta signalling pathway. Br. J. Cancer 2015, 112, 1367–1375. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  102. Lipchina, I.; Elkabetz, Y.; Hafner, M.; Sheridan, R.; Mihailovic, A.; Tuschl, T.; Sander, C.; Studer, L.; Betel, D. Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes. Dev. 2011, 25, 2173–2186. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  103. Lipchina, I.; Studer, L.; Betel, D. The expanding role of miR-302-367 in pluripotency and reprogramming. Cell Cycle 2012, 11, 1517–1523. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  104. Lin, S.L.; Chang, D.C.; Lin, C.H.; Ying, S.Y.; Leu, D.; Wu, D.T. Regulation of somatic cell reprogramming through inducible mir-302 expression. Nucleic Acids Res. 2011, 39, 1054–1065. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  105. Lee, M.R.; Prasain, N.; Chae, H.D.; Kim, Y.J.; Mantel, C.; Yoder, M.C.; Broxmeyer, H.E. Epigenetic regulation of NANOG by miR-302 cluster-MBD2 completes induced pluripotent stem cell reprogramming. Stem Cells 2013, 31, 666–681. [Google Scholar] [CrossRef] [Green Version]
  106. Bentwich, I.; Avniel, A.; Karov, Y.; Aharonov, R.; Gilad, S.; Barad, O.; Barzilai, A.; Einat, P.; Einav, U.; Meiri, E.; et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 2005, 37, 766–770. [Google Scholar] [CrossRef]
  107. Lehnert, S.; Van Loo, P.; Thilakarathne, P.J.; Marynen, P.; Verbeke, G.; Schuit, F.C. Evidence for co-evolution between human microRNAs and Alu-repeats. PLoS ONE 2009, 4, e4456. [Google Scholar] [CrossRef] [Green Version]
  108. Bortolin-Cavaille, M.L.; Dance, M.; Weber, M.; Cavaille, J. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 2009, 37, 3464–3473. [Google Scholar] [CrossRef]
  109. Zhang, R.; Wang, Y.Q.; Su, B. Molecular evolution of a primate-specific microRNA family. Mol. Biol. Evol. 2008, 25, 1493–1502. [Google Scholar] [CrossRef] [Green Version]
  110. Noguer-Dance, M.; Abu-Amero, S.; Al-Khtib, M.; Lefevre, A.; Coullin, P.; Moore, G.E.; Cavaille, J. The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta. Hum. Mol. Genet. 2010, 19, 3566–3582. [Google Scholar] [CrossRef] [Green Version]
  111. Fothi, A.; Biro, O.; Erdei, Z.; Apati, A.; Orban, T.I. Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster. RNA Biol. 2021, 18, 1170–1180. [Google Scholar] [CrossRef] [PubMed]
  112. Donker, R.B.; Mouillet, J.F.; Chu, T.; Hubel, C.A.; Stolz, D.B.; Morelli, A.E.; Sadovsky, Y. The expression profile of C19MC microRNAs in primary human trophoblast cells and exosomes. Mol. Hum. Reprod. 2012, 18, 417–424. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  113. Stadler, B.; Ivanovska, I.; Mehta, K.; Song, S.; Nelson, A.; Tan, Y.; Mathieu, J.; Darby, C.; Blau, C.A.; Ware, C.; et al. Characterization of microRNAs involved in embryonic stem cell states. Stem Cells Dev. 2010, 19, 935–950. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  114. Ren, J.; Jin, P.; Wang, E.; Marincola, F.M.; Stroncek, D.F. MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells. J. Transl. Med. 2009, 7, 20. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  115. Kobayashi, N.; Okae, H.; Hiura, H.; Kubota, N.; Kobayashi, E.H.; Shibata, S.; Oike, A.; Hori, T.; Kikutake, C.; Hamada, H.; et al. The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells. Nat. Commun. 2022, 13, 3071. [Google Scholar] [CrossRef]
  116. Nguyen, P.N.N.; Choo, K.B.; Huang, C.J.; Sugii, S.; Cheong, S.K.; Kamarul, T. miR-524-5p of the primate-specific C19MC miRNA cluster targets TP53IPN1- and EMT-associated genes to regulate cellular reprogramming. Stem Cell Res. Ther. 2017, 8, 214. [Google Scholar] [CrossRef]
  117. Mong, E.F.; Yang, Y.; Akat, K.M.; Canfield, J.; VanWye, J.; Lockhart, J.; Tsibris, J.C.M.; Schatz, F.; Lockwood, C.J.; Tuschl, T.; et al. Chromosome 19 microRNA cluster enhances cell reprogramming by inhibiting epithelial-to-mesenchymal transition. Sci. Rep. 2020, 10, 3029. [Google Scholar] [CrossRef] [Green Version]
  118. Jinesh, G.G.; Flores, E.R.; Brohl, A.S. Chromosome 19 miRNA cluster and CEBPB expression specifically mark and potentially drive triple negative breast cancers. PLoS ONE 2018, 13, e0206008. [Google Scholar] [CrossRef] [Green Version]
  119. Fornari, F.; Milazzo, M.; Chieco, P.; Negrini, M.; Marasco, E.; Capranico, G.; Mantovani, V.; Marinello, J.; Sabbioni, S.; Callegari, E.; et al. In hepatocellular carcinoma miR-519d is up-regulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2. J. Pathol. 2012, 227, 275–285. [Google Scholar] [CrossRef]
  120. Augello, C.; Vaira, V.; Caruso, L.; Destro, A.; Maggioni, M.; Park, Y.N.; Montorsi, M.; Santambrogio, R.; Roncalli, M.; Bosari, S. MicroRNA profiling of hepatocarcinogenesis identifies C19MC cluster as a novel prognostic biomarker in hepatocellular carcinoma. Liver Int. 2012, 32, 772–782. [Google Scholar] [CrossRef]
  121. Kleinman, C.L.; Gerges, N.; Papillon-Cavanagh, S.; Sin-Chan, P.; Pramatarova, A.; Quang, D.A.; Adoue, V.; Busche, S.; Caron, M.; Djambazian, H.; et al. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat. Genet. 2014, 46, 39–44. [Google Scholar] [CrossRef]
  122. Strub, G.M.; Kirsh, A.L.; Whipple, M.E.; Kuo, W.P.; Keller, R.B.; Kapur, R.P.; Majesky, M.W.; Perkins, J.A. Endothelial and circulating C19MC microRNAs are biomarkers of infantile hemangioma. JCI Insight 2016, 1, e88856. [Google Scholar] [CrossRef] [Green Version]
  123. Flor, I.; Spiekermann, M.; Loning, T.; Dieckmann, K.P.; Belge, G.; Bullerdiek, J. Expression of microRNAs of C19MC in Different Histological Types of Testicular Germ Cell Tumour. Cancer Genom. Proteom. 2016, 13, 281–289. [Google Scholar]
  124. Vaira, V.; Elli, F.; Forno, I.; Guarnieri, V.; Verdelli, C.; Ferrero, S.; Scillitani, A.; Vicentini, L.; Cetani, F.; Mantovani, G.; et al. The microRNA cluster C19MC is deregulated in parathyroid tumours. J. Mol. Endocrinol. 2012, 49, 115–124. [Google Scholar] [CrossRef] [Green Version]
  125. Rippe, V.; Dittberner, L.; Lorenz, V.N.; Drieschner, N.; Nimzyk, R.; Sendt, W.; Junker, K.; Belge, G.; Bullerdiek, J. The two stem cell microRNA gene clusters C19MC and miR-371-3 are activated by specific chromosomal rearrangements in a subgroup of thyroid adenomas. PLoS ONE 2010, 5, e9485. [Google Scholar] [CrossRef]
  126. Buganim, Y.; Faddah, D.A.; Jaenisch, R. Mechanisms and models of somatic cell reprogramming. Nat. Rev. Genet. 2013, 14, 427–439. [Google Scholar] [CrossRef] [Green Version]
  127. David, L.; Polo, J.M. Phases of reprogramming. Stem Cell Res. 2014, 12, 754–761. [Google Scholar] [CrossRef] [Green Version]
  128. Houbaviy, H.B.; Dennis, L.; Jaenisch, R.; Sharp, P.A. Characterization of a highly variable eutherian microRNA gene. RNA 2005, 11, 1245–1257. [Google Scholar] [CrossRef] [Green Version]
  129. Eddy, S.R.; Mitchison, G.; Durbin, R. Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol. 1995, 2, 9–23. [Google Scholar] [CrossRef]
  130. Calabrese, J.M.; Seila, A.C.; Yeo, G.W.; Sharp, P.A. RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 2007, 104, 18097–18102. [Google Scholar] [CrossRef]
  131. Tata, P.R.; Tata, N.R.; Kuhl, M.; Sirbu, I.O. Identification of a novel epigenetic regulatory region within the pluripotency associated microRNA cluster, EEmiRC. Nucleic Acids Res. 2011, 39, 3574–3581. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  132. Chen, X.; Xu, H.; Yuan, P.; Fang, F.; Huss, M.; Vega, V.B.; Wong, E.; Orlov, Y.L.; Zhang, W.; Jiang, J.; et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133, 1106–1117. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  133. Voorhoeve, P.M.; le Sage, C.; Schrier, M.; Gillis, A.J.; Stoop, H.; Nagel, R.; Liu, Y.P.; van Duijse, J.; Drost, J.; Griekspoor, A.; et al. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 2006, 124, 1169–1181. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  134. Pan, B.; He, B.; Xu, X.; Liu, X.; Xu, T.; Xu, M.; Chen, X.; Zeng, K.; Lin, K.; Hu, X.; et al. MicroRNA-371-3 cluster as biomarkers for the diagnosis and prognosis of cancers. Cancer Manag. Res. 2019, 11, 5437–5457. [Google Scholar] [CrossRef] [Green Version]
  135. Chen, K.; Rajewsky, N. The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet. 2007, 8, 93–103. [Google Scholar] [CrossRef]
  136. Chen, L.; Heikkinen, L.; Emily Knott, K.; Liang, Y.; Wong, G. Evolutionary conservation and function of the human embryonic stem cell specific miR-302/367 cluster. Comp. Biochem. Physiol. Part. D Genom. Proteom. 2015, 16, 83–98. [Google Scholar] [CrossRef] [Green Version]
  137. Mohammed, J.; Siepel, A.; Lai, E.C. Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. RNA 2014, 20, 1850–1863. [Google Scholar] [CrossRef] [Green Version]
  138. Huang, Q.; Gumireddy, K.; Schrier, M.; le Sage, C.; Nagel, R.; Nair, S.; Egan, D.A.; Li, A.; Huang, G.; Klein-Szanto, A.J.; et al. The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat. Cell Biol. 2008, 10, 202–210. [Google Scholar] [CrossRef]
  139. Liu, P.; Wilson, M.J. miR-520c and miR-373 upregulate MMP9 expression by targeting mTOR and SIRT1, and activate the Ras/Raf/MEK/Erk signaling pathway and NF-kappaB factor in human fibrosarcoma cells. J. Cell Physiol. 2012, 227, 867–876. [Google Scholar] [CrossRef] [Green Version]
  140. Keklikoglou, I.; Koerner, C.; Schmidt, C.; Zhang, J.D.; Heckmann, D.; Shavinskaya, A.; Allgayer, H.; Guckel, B.; Fehm, T.; Schneeweiss, A.; et al. MicroRNA-520/373 family functions as a tumor suppressor in estrogen receptor negative breast cancer by targeting NF-kappaB and TGF-beta signaling pathways. Oncogene 2012, 31, 4150–4163. [Google Scholar] [CrossRef]
  141. Wu, S.; Aksoy, M.; Shi, J.; Houbaviy, H.B. Evolution of the miR-290-295/miR-371-373 cluster family seed repertoire. PLoS ONE 2014, 9, e108519. [Google Scholar] [CrossRef]
  142. Judson, R.L.; Babiarz, J.E.; Venere, M.; Blelloch, R. Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat. Biotechnol. 2009, 27, 459–461. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  143. Morin, R.D.; O’Connor, M.D.; Griffith, M.; Kuchenbauer, F.; Delaney, A.; Prabhu, A.L.; Zhao, Y.; McDonald, H.; Zeng, T.; Hirst, M.; et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008, 18, 610–621. [Google Scholar] [CrossRef] [Green Version]
  144. Subramanyam, D.; Lamouille, S.; Judson, R.L.; Liu, J.Y.; Bucay, N.; Derynck, R.; Blelloch, R. Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat. Biotechnol. 2011, 29, 443–448. [Google Scholar] [CrossRef]
  145. Dalton, S. Exposing hidden dimensions of embryonic stem cell cycle control. Cell Stem Cell 2009, 4, 9–10. [Google Scholar] [CrossRef] [Green Version]
  146. Gonzales, K.A.; Liang, H.; Lim, Y.S.; Chan, Y.S.; Yeo, J.C.; Tan, C.P.; Gao, B.; Le, B.; Tan, Z.Y.; Low, K.Y.; et al. Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways. Cell 2015, 162, 564–579. [Google Scholar] [CrossRef] [Green Version]
  147. Benetti, R.; Gonzalo, S.; Jaco, I.; Munoz, P.; Gonzalez, S.; Schoeftner, S.; Murchison, E.; Andl, T.; Chen, T.; Klatt, P.; et al. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat. Struct. Mol. Biol. 2008, 15, 268–279. [Google Scholar] [CrossRef]
  148. Yuan, K.; Ai, W.B.; Wan, L.Y.; Tan, X.; Wu, J.F. The miR-290-295 cluster as multi-faceted players in mouse embryonic stem cells. Cell Biosci. 2017, 7, 38. [Google Scholar] [CrossRef] [Green Version]
  149. Niehrs, C. Function and biological roles of the Dickkopf family of Wnt modulators. Oncogene 2006, 25, 7469–7481. [Google Scholar] [CrossRef] [Green Version]
  150. Zovoilis, A.; Smorag, L.; Pantazi, A.; Engel, W. Members of the miR-290 cluster modulate in vitro differentiation of mouse embryonic stem cells. Differentiation 2009, 78, 69–78. [Google Scholar] [CrossRef]
  151. Gu, K.L.; Zhang, Q.; Yan, Y.; Li, T.T.; Duan, F.F.; Hao, J.; Wang, X.W.; Shi, M.; Wu, D.R.; Guo, W.T.; et al. Pluripotency-associated miR-290/302 family of microRNAs promote the dismantling of naive pluripotency. Cell Res. 2016, 26, 350–366. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  152. Graham, B.; Marcais, A.; Dharmalingam, G.; Carroll, T.; Kanellopoulou, C.; Graumann, J.; Nesterova, T.B.; Bermange, A.; Brazauskas, P.; Xella, B.; et al. MicroRNAs of the miR-290-295 Family Maintain Bivalency in Mouse Embryonic Stem Cells. Stem Cell Rep. 2016, 6, 635–642. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  153. Kanellopoulou, C.; Gilpatrick, T.; Kilaru, G.; Burr, P.; Nguyen, C.K.; Morawski, A.; Lenardo, M.J.; Muljo, S.A. Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l. Stem Cell Rep. 2015, 5, 971–978. [Google Scholar] [CrossRef] [Green Version]
  154. Zhou, A.D.; Diao, L.T.; Xu, H.; Xiao, Z.D.; Li, J.H.; Zhou, H.; Qu, L.H. beta-Catenin/LEF1 transactivates the microRNA-371-373 cluster that modulates the Wnt/beta-catenin-signaling pathway. Oncogene 2012, 31, 2968–2978. [Google Scholar] [CrossRef] [Green Version]
  155. Cao, Y.; Guo, W.T.; Tian, S.; He, X.; Wang, X.W.; Liu, X.; Gu, K.L.; Ma, X.; Huang, D.; Hu, L.; et al. miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency. EMBO J. 2015, 34, 609–623. [Google Scholar] [CrossRef] [Green Version]
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Figure 1. Genome organization and multiple sequence alignment of miR-302/367 precursor coding regions in humans, mice, rabbits, and chickens. (a) Humans, mice, rabbits, and chikens exhibit a common cluster structure, comprising four miR-302s and one miR-367. Interestingly, chikens express an extra miRNA, gga-miR-1811, within the miR-302/367 cluster. (b) Multiple sequence alignment of miR-302/367 precursor coding regions in humans, mice, rabbits, and chickens represent high similarity of this cluster. The seed sequences are highlighted in yellow; mismatches are shown in red. Mature -5p and -3p miRNA sequences are shown in blue. Mature sequence of gga-miR-1811 is shown in green. The asterisks indicate sequence homology.
Figure 1. Genome organization and multiple sequence alignment of miR-302/367 precursor coding regions in humans, mice, rabbits, and chickens. (a) Humans, mice, rabbits, and chikens exhibit a common cluster structure, comprising four miR-302s and one miR-367. Interestingly, chikens express an extra miRNA, gga-miR-1811, within the miR-302/367 cluster. (b) Multiple sequence alignment of miR-302/367 precursor coding regions in humans, mice, rabbits, and chickens represent high similarity of this cluster. The seed sequences are highlighted in yellow; mismatches are shown in red. Mature -5p and -3p miRNA sequences are shown in blue. Mature sequence of gga-miR-1811 is shown in green. The asterisks indicate sequence homology.
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Figure 2. Main targets of miR-302/367 cluster. The miR-302-367 cluster plays a central role in maintaining ESC pluripotency and self-renewal by regulating different signaling pathways. The cytoplasmic mature miR-302/367 gene products positively regulate self-renewal by modulating G1/S transition through direct targeting of the cell cycle regulators, such as CYCLIN D1/D2 and CDK4/6. Additionally, they promote S phase entry via an alternative Rb-independent pathway. These mature miRNA products also maintain the pluripotency of ESCs by targeting Nodal/Activin inhibitors, such as LEFTY. They also promote BMP signaling through direct targeting of BMP inhibitors (TOB2, DAZAP2, and SLAIN1), thus maintain pluripotency by repressing neural differentiation. Moreover, miR-302/367 members promote reprogramming and iPS cell establishment through induction of global DNA demethylation by post-transcriptional suppression of epigenetic regulators such as AOF1/2, MECP1/2, and MBD2.
Figure 2. Main targets of miR-302/367 cluster. The miR-302-367 cluster plays a central role in maintaining ESC pluripotency and self-renewal by regulating different signaling pathways. The cytoplasmic mature miR-302/367 gene products positively regulate self-renewal by modulating G1/S transition through direct targeting of the cell cycle regulators, such as CYCLIN D1/D2 and CDK4/6. Additionally, they promote S phase entry via an alternative Rb-independent pathway. These mature miRNA products also maintain the pluripotency of ESCs by targeting Nodal/Activin inhibitors, such as LEFTY. They also promote BMP signaling through direct targeting of BMP inhibitors (TOB2, DAZAP2, and SLAIN1), thus maintain pluripotency by repressing neural differentiation. Moreover, miR-302/367 members promote reprogramming and iPS cell establishment through induction of global DNA demethylation by post-transcriptional suppression of epigenetic regulators such as AOF1/2, MECP1/2, and MBD2.
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Figure 3. Genome organization and multiple sequence alignment of human C19MC cluster and three rabbit homologs. (a) Three rabbit homologues pre-miRNAs of human C19MC including ocu-miR-512, ocu-miR-498, and ocu-miR-520e are located on contig ChrUn0226 in same order as human C19MC on Chr.19. (b) Multiple sequence alignment represented high sequence similarity of rabbit mature miRNAs with their human homologues. Ocu-miR-520e shares the common consensus seed sequence of “AAGTGCT” with its human homologs, but ocu-miR-512 harbors a slightly different seed sequence. The seed sequences are highlighted in yellow. Mismatches in seed sequences are shown in red. The asterisks indicate sequence homology.
Figure 3. Genome organization and multiple sequence alignment of human C19MC cluster and three rabbit homologs. (a) Three rabbit homologues pre-miRNAs of human C19MC including ocu-miR-512, ocu-miR-498, and ocu-miR-520e are located on contig ChrUn0226 in same order as human C19MC on Chr.19. (b) Multiple sequence alignment represented high sequence similarity of rabbit mature miRNAs with their human homologues. Ocu-miR-520e shares the common consensus seed sequence of “AAGTGCT” with its human homologs, but ocu-miR-512 harbors a slightly different seed sequence. The seed sequences are highlighted in yellow. Mismatches in seed sequences are shown in red. The asterisks indicate sequence homology.
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Figure 4. Genome organization and multiple sequence alignment of mmu-miR-290/295, ocu-miR-290/295, and hsa-miR-371/373 precursors in mice, humans, and rabbits. (a) miR-371/373, a human ortholog of the mmu-miR-290/295 cluster, is located in close proximity to C19MC on chromosome 19 and comprises of four pre-miRNAs. Rabbit homologs of the mmu-miR-290/295 cluster are located on the reverse strand of a short pseudo-chromosome (chrUn0226) and are comprised of three mature miRNAs. Similar to hsa-miR-371/373, the ocu-miR290/295 cluster is located 3′ to the rabbit C19MC. (b) All pre-miRNAs of mmu-miR-290/295 and hsa-miR-371/373 share ESC-specific seed sequence of “AAGTGC” except for mmu- miR-293 pre-miRNA. From rabbit cluster only ocu-miR-294 contains the same seed sequence. The seed sequences are highlighted in yellow. Mismatches in seed sequences are shown in red. Mature -5p and -3p miRNA sequences are shown in blue. The asterisks indicate sequence homology.
Figure 4. Genome organization and multiple sequence alignment of mmu-miR-290/295, ocu-miR-290/295, and hsa-miR-371/373 precursors in mice, humans, and rabbits. (a) miR-371/373, a human ortholog of the mmu-miR-290/295 cluster, is located in close proximity to C19MC on chromosome 19 and comprises of four pre-miRNAs. Rabbit homologs of the mmu-miR-290/295 cluster are located on the reverse strand of a short pseudo-chromosome (chrUn0226) and are comprised of three mature miRNAs. Similar to hsa-miR-371/373, the ocu-miR290/295 cluster is located 3′ to the rabbit C19MC. (b) All pre-miRNAs of mmu-miR-290/295 and hsa-miR-371/373 share ESC-specific seed sequence of “AAGTGC” except for mmu- miR-293 pre-miRNA. From rabbit cluster only ocu-miR-294 contains the same seed sequence. The seed sequences are highlighted in yellow. Mismatches in seed sequences are shown in red. Mature -5p and -3p miRNA sequences are shown in blue. The asterisks indicate sequence homology.
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Figure 5. Main targets of miR-290/294 cluster. The miR-290/295 cluster modulates both stemness and differentiation characteristics of mouse ESCs and embryos by regulating cell cycle, de novo DNA methylation, apoptosis, and transcription of pluripotent-associated transcription factors. The cytoplasmic mature miR-290/295 members maintain pluripotency of mESC by accelerating G1 and extending S phase through direct targeting of cell cycle inhibitors such as p21, Lats2, Wee1, and Fbxl5, and also repressing S/G2 transition. These mature miRNAs also incorporate Prc2, Ezh2 and Suz12 into promoters of bivalent differentiation genes. The miR-290/295 cluster together with miR-302/376 promote transition from naïve to primed pluripotency by enhancing the activity of MEK pathway through direct repression of Akt1. These mature miRNAs partially favor pluripotency upon differentiation by direct targeting of Dkk-1, a Wnt pathway inhibitor, resulting in upregulation of c-Myc. The mature miR-290/295 gene products also modulate DNA methylation in the pre-implantation embryos by targeting of Rbl2 and subsequent inhibition of Dnmt3b. The miR-290/295 cluster also enhances the reprogramming of somatic cells and the quality of mouse iPSCs through post-transcriptional suppression of Ash1l expression and consequently downregulation of HOX genes, which in turn promote reprogramming through polycomb-mediated gene silencing.
Figure 5. Main targets of miR-290/294 cluster. The miR-290/295 cluster modulates both stemness and differentiation characteristics of mouse ESCs and embryos by regulating cell cycle, de novo DNA methylation, apoptosis, and transcription of pluripotent-associated transcription factors. The cytoplasmic mature miR-290/295 members maintain pluripotency of mESC by accelerating G1 and extending S phase through direct targeting of cell cycle inhibitors such as p21, Lats2, Wee1, and Fbxl5, and also repressing S/G2 transition. These mature miRNAs also incorporate Prc2, Ezh2 and Suz12 into promoters of bivalent differentiation genes. The miR-290/295 cluster together with miR-302/376 promote transition from naïve to primed pluripotency by enhancing the activity of MEK pathway through direct repression of Akt1. These mature miRNAs partially favor pluripotency upon differentiation by direct targeting of Dkk-1, a Wnt pathway inhibitor, resulting in upregulation of c-Myc. The mature miR-290/295 gene products also modulate DNA methylation in the pre-implantation embryos by targeting of Rbl2 and subsequent inhibition of Dnmt3b. The miR-290/295 cluster also enhances the reprogramming of somatic cells and the quality of mouse iPSCs through post-transcriptional suppression of Ash1l expression and consequently downregulation of HOX genes, which in turn promote reprogramming through polycomb-mediated gene silencing.
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Table
Table 1. Summary of ESC-specific miRNAs and their relative function.
Table 1. Summary of ESC-specific miRNAs and their relative function.
Cell TypemiRNAsExpression LevelFunctionSignaling PathwaysTargets
Mouse ESCsmiR-302/367 clusterLow expressionRegulation of pluripotency,
self-renewal, and reprogramming		Cdkn1a [61]
TGF-β signaling pathway
BMP signaling pathway		NA
Lats2 [95]
miR-290/295 clusterHigh expressionRegulation of cell cycle progression
and
naïve pluripotency		ATM/ATR chek2-p53
pathway
Wnt signaling pathway
MEK Pathway activation		Cyclin D1, p21, Lats2 [67,146]
Dkk-1 [150]
Akt1 [151]
Early phases of differentiationDNA methylation
HOX gene inactivation		Rbl2 [62,147]
Ash1l [153]
Human ESCsmiR-302/367 clusterHigh expressionRegulation of pluripotency, self-renewal, and reprogrammingCyclin D1/D2 and Cdk2 [68]
Nodal–Activin pathway		LEFTY [98,99,100]
BNIP3L/Nix [97]
miR-371/373 clusterHigh expressionCell cycle regulation 
Reprogramming		G1/S transition
P53 pathway		P21 [70]
MBD2 [155]
C19MCHigh expression in naïve hESCs
and iPCs		Pluripotency maintenanceChromatin structure modification pathway [114]NA
Prevent differentiationECM- related pathway [115]NA
Derivation and maintenance of human trophoblast stem cellsP53 pathwayCCNG2 DKN1A PMAIP1 ZMAT3 TP53INP1 [115]
Rabbit ES-like cellsmiR-302/367 clusterHigh expressionRegulation of pluripotency and self-renewalNodal–Activin pathwayLefty [47]
miR-290/295 clusterLow expressionEarly embryonic developmentNANA
C19MCLow expressionEarly embryonic developmentNANA
Chicken PGC linemiR-302b
miR-302a		High expressionCell proliferation
Prevent differentiation		Glycolysis metabolism
Somatic gene silencing		Gpi3 [92]
Sox11 [91]
NA: not addressed.
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Maraghechi, P.; Aponte, M.T.S.; Ecker, A.; Lázár, B.; Tóth, R.; Szabadi, N.T.; Gócza, E. Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells. Genes 2023, 14, 1434. https://doi.org/10.3390/genes14071434

AMA Style

Maraghechi P, Aponte MTS, Ecker A, Lázár B, Tóth R, Szabadi NT, Gócza E. Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells. Genes. 2023; 14(7):1434. https://doi.org/10.3390/genes14071434

Chicago/Turabian Style

Maraghechi, Pouneh, Maria Teresa Salinas Aponte, András Ecker, Bence Lázár, Roland Tóth, Nikolett Tokodyné Szabadi, and Elen Gócza. 2023. "Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells" Genes 14, no. 7: 1434. https://doi.org/10.3390/genes14071434

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