Skip to main content
SpringerLink
Log in

Genomic Regulation of MicroRNA Expression in Disease Development

  • Protocol
  • First Online:
Book cover Bioinformatics in MicroRNA Research

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1617))

Abstract

MiroRNAs (miRNAs) are an abundant class of regulators of gene expression . Through base paring with messenger RNAs, miRNAs repress the expression levels of other genes, including those encoding transcription factors. On the other hand, the spatial and temporal patterns of miRNAs transcription are subject to regulation by transcription factors. The inter-regulation between miRNAs and TFs integrates two gene regulatory networks—at transcriptional level and post-transcriptional level to fine-tune the gene expression pattern in the development of multicellular organisms. Aberrant regulation at either of these two levels of gene regulation can lead to developmental disorder and disease.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(Database issue):D68–D73

    Article  CAS  PubMed  Google Scholar 

  2. Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6(5):376–385

    Article  CAS  PubMed  Google Scholar 

  3. Friedman RC et al (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1):92–105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Chiang HR et al (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24(10):992–1009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10(12):1957–1966

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lee Y et al (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Pfeffer S et al (2005) Identification of microRNAs of the herpesvirus family. Nat Methods 2(4):269–276

    Article  CAS  PubMed  Google Scholar 

  8. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72:449–479

    Article  CAS  PubMed  Google Scholar 

  9. Levine M, Cattoglio C, Tjian R (2014) Looping back to leap forward: transcription enters a new era. Cell 157(1):13–25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Levine M (2010) Transcriptional enhancers in animal development and evolution. Curr Biol 20(17):R754–R763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Reinhart BJ et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403(6772):901–906

    Article  CAS  PubMed  Google Scholar 

  12. Johnson SM, Lin SY, Slack FJ (2003) The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev Biol 259(2):364–379

    Article  CAS  PubMed  Google Scholar 

  13. Kai ZS et al (2013) Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Dev Biol 374(1):223–233

    Article  CAS  PubMed  Google Scholar 

  14. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11(9):597–610

    CAS  PubMed  Google Scholar 

  15. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8(6):450–461

    Article  CAS  PubMed  Google Scholar 

  16. Hobert O (2006) Architecture of a microRNA-controlled gene regulatory network that diversifies neuronal cell fates. Cold Spring Harb Symp Quant Biol 71:181–188

    Article  CAS  PubMed  Google Scholar 

  17. Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426(6968):845–849

    Article  CAS  PubMed  Google Scholar 

  18. Hobert O (2004) Common logic of transcription factor and microRNA action. Trends Biochem Sci 29(9):462–468

    Article  CAS  PubMed  Google Scholar 

  19. Posadas DM, Carthew RW (2014) MicroRNAs and their roles in developmental canalization. Curr Opin Genet Dev 27:1–6

    Article  CAS  PubMed  Google Scholar 

  20. Li X et al (2009) A microRNA imparts robustness against environmental fluctuation during development. Cell 137(2):273–282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kennell JA et al (2012) The microRNA miR-8 is a positive regulator of pigmentation and eclosion in Drosophila. Dev Dyn 241(1):161–168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Im HI, Kenny PJ (2012) MicroRNAs in neuronal function and dysfunction. Trends Neurosci 35(5):325–334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lujambio A, Lowe SW (2012) The microcosmos of cancer. Nature 482(7385):347–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zhao Y et al (2007) Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 129(2):303–317

    Article  CAS  PubMed  Google Scholar 

  25. Agarwal V et al (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4:e05005

    Article  PubMed Central  Google Scholar 

  26. Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74

    Article  Google Scholar 

  27. Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155(1):39–55

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Research Center for Translational Medicine (Shanghai), Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Science and Education Plaza, 197 Rui Jin Er Road, Shanghai, 200025, China

    Feng Liu Ph.D.

Authors
  1. Feng Liu Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Feng Liu Ph.D. .

Editor information

Editors and Affiliations

  1. School of Computing, University of South Alabama, Mobile, Alabama, USA

    Jingshan Huang

  2. Department of Pharmacology, University of South Alabama, Mobile, Alabama, USA

    Glen M. Borchert

  3. Department of Computer and Information Science, University of Oregon, Eugene, Oregon, USA

    Dejing Dou

  4. Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, Kansas, USA

    Jun (Luke) Huan

  5. School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China

    Wenjun Lan

  6. Mitchel Cancer Institute, University of South Alabama, Mobile, Alabama, USA

    Ming Tan

  7. Department of Endocrinology, First Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China

    Bin Wu

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Liu, F. (2017). Genomic Regulation of MicroRNA Expression in Disease Development. In: Huang, J., et al. Bioinformatics in MicroRNA Research. Methods in Molecular Biology, vol 1617. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7046-9_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7046-9_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7044-5

  • Online ISBN: 978-1-4939-7046-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation