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miRNomics pp 423–438Cite as

44 Current Challenges in miRNomics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2257))

Abstract

Mature microRNAs (miRNAs) are short RNA sequences about 18–24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5′ UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future.

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Author information

Authors and Affiliations

  1. Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey

    Bünyamin Akgül

  2. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

  3. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany

    Peter F. Stadler

  4. Institute for Theoretical Chemistry, University of Vienna, Wien, Austria

    Peter F. Stadler

  5. Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia

    Peter F. Stadler

  6. Santa Fe Institute, Santa Fe, NM, USA

    Peter F. Stadler

  7. Department of Biology, Carleton University, Ottawa, ON, Canada

    Liam J. Hawkins, Hanane Hadj-Moussa & Kenneth B. Storey

  8. Department of Histology and Embryology, Medical Faculty, Aydın Adnan Menderes University, Aydın, Turkey

    Kemal Ergin

  9. Department of Basic Oncology and Cancer Biology, Institute of Health Sciences, Aydın Adnan Menderes University, Aydın, Turkey

    Kemal Ergin & Rahmi Çetinkaya

  10. Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil

    Alexandre R. Paschoal

  11. Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil

    Pedro G. Nachtigall

  12. Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey

    Yusuf Tutar

  13. Department of Information System, Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel

    Malik Yousef

  14. Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, Mülheim adR, Germany

    Jens Allmer

Authors
  1. Bünyamin Akgül
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  2. Peter F. Stadler
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  3. Liam J. Hawkins
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  4. Hanane Hadj-Moussa
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  5. Kenneth B. Storey
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  6. Kemal Ergin
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  7. Rahmi Çetinkaya
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  8. Alexandre R. Paschoal
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  9. Pedro G. Nachtigall
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  10. Yusuf Tutar
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  11. Malik Yousef
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  12. Jens Allmer
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Corresponding author

Correspondence to Jens Allmer .

Editor information

Editors and Affiliations

  1. Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, Mülheim adR, Germany

    Jens Allmer

  2. Department of Information System, Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel

    Malik Yousef

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Akgül, B. et al. (2022). 44 Current Challenges in miRNomics. In: Allmer, J., Yousef, M. (eds) miRNomics. Methods in Molecular Biology, vol 2257. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1170-8_19

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  • DOI: https://doi.org/10.1007/978-1-0716-1170-8_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1169-2

  • Online ISBN: 978-1-0716-1170-8

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