Skip to main content

Identifying RBP Targets with RIP-seq

  • Protocol
Post-Transcriptional Gene Regulation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1358))

Abstract

Throughout their lifetime RNA molecules interact with a variety of RNA-binding proteins (RBPs). RBPs control gene expression by regulating splicing, polyadenylation, editing, transport, stability, and translation of RNA. There are ~1500 RBPs encoded by the human genome and recent studies have detected ~1100 proteins directly interacting with polyadenylated RNA. Identifying the RNAs bound by RBPs will continue to provide important insights into the regulation of gene expression.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Gerstberger S, Hafner M, Tuschl T (2014) A census of human RNA-binding proteins. Nat Rev Genet 15:829–845

    Article  CAS  PubMed  Google Scholar 

  2. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149:1393–1406

    Article  CAS  PubMed  Google Scholar 

  3. Baltz AG, Munschauer M, Schwanhausser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M (2012) The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 46:674–690

    Article  CAS  PubMed  Google Scholar 

  4. Gao FB, Carson CC, Levine T, Keene JD (1994) Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1. Proc Natl Acad Sci U S A 91:11207–11211

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Keene JD, Komisarow JM, Friedersdorf MB (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1:302–307

    Article  CAS  PubMed  Google Scholar 

  6. Tenenbaum SA, Carson CC, Lager PJ, Keene JD (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A 97:14085–14090

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302:1212–1215

    Article  CAS  PubMed  Google Scholar 

  8. Singh G, Ricci EP, Moore MJ (2014) RIPiT-Seq: a high-throughput approach for footprinting RNA:protein complexes. Methods 65:320–332

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M Jr, Tuschl T, Ohler U, Keene JD (2011) Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 43:327–339

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Mili S, Steitz JA (2004) Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10:1692–1694

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD (2012) Site identification in high-throughput RNA-protein interaction data. Bioinformatics (Oxford, England) 28:3013–3020

    Article  CAS  Google Scholar 

  12. Kucukural A, Ozadam H, Singh G, Moore MJ, Cenik C (2013) ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics (Oxford, England) 29:2485–2486

    Article  CAS  Google Scholar 

  13. Li Y, Zhao DY, Greenblatt JF, Zhang Z (2013) RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res 41, e94

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Neelanjan Mukherjee .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Wessels, HH., Hirsekorn, A., Ohler, U., Mukherjee, N. (2016). Identifying RBP Targets with RIP-seq. In: Dassi, E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 1358. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3067-8_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-3067-8_9

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3066-1

  • Online ISBN: 978-1-4939-3067-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics