Skip to main content

Small RNA Library Cloning Procedure for Deep Sequencing of Specific Endogenous siRNA Classes in Caenorhabditis elegans

  • Protocol
  • First Online:
Animal Endo-SiRNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1173))

Abstract

In recent years, distinct classes of small RNAs ranging in size from ~21 to 26 nucleotides have been discovered and shown to play important roles in a wide array of cellular functions. Because of the abundance of these small RNAs, library preparation from an RNA sample followed by deep sequencing provides the identity and quantity of a particular class of small RNAs. In this chapter we describe a detailed protocol for preparing small RNA libraries for deep sequencing on the Illumina platform from the nematode C. elegans.

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 119.00
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. Sabin LR, Delas MJ, Hannon GJ (2013) Dogma derailed: the many influences of RNA on the genome. Mol Cell 49:783–794

    Article  CAS  PubMed  Google Scholar 

  2. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139

    Article  CAS  PubMed  Google Scholar 

  3. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Shirayama M, Seth M, Lee HC et al (2012) piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150:65–77

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Ashe A, Sapetschnig A, Weick EM et al (2012) piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150:88–99

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Pak J, Fire A (2007) Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315:241–244

    Article  CAS  PubMed  Google Scholar 

  7. Sijen T, Steiner FA, Thijssen KL et al (2007) Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315:244–247

    Article  CAS  PubMed  Google Scholar 

  8. Pak J, Maniar JM, Mello CC et al (2012) Protection from feed-forward amplification in an amplified RNAi mechanism. Cell 151:885–899

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Boisvert ME, Simard MJ (2008) RNAi pathway in C. elegans: the argonautes and collaborators. Curr Top Microbiol Immunol 320:21–36

    CAS  PubMed  Google Scholar 

  10. van Wolfswinkel JC, Ketting RF (2010) The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci 123:1825–1839

    Article  PubMed  Google Scholar 

  11. Gent JI, Lamm AT, Pavelec DM et al (2010) Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol Cell 37:679–689

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Conine CC, Batista PJ, Gu W et al (2010) Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc Natl Acad Sci U S A 107:3588–3593

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Burkhart KB, Guang S, Buckley BA et al (2011) Pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation. PLoS Genet 7:e1002249

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Guang S, Bochner AF, Pavelec DM et al (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321:537–541

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Ruby JG, Jan C, Player C et al (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  CAS  PubMed  Google Scholar 

  16. Claycomb JM, Batista PJ, Pang KM et al (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139:123–134

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Gu W, Shirayama M, Conte D Jr et al (2009) Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell 36:231–244

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Hall SE, Chirn GW, Lau NC et al (2013) RNAi pathways contribute to developmental history-dependent phenotypic plasticity in C. elegans. RNA 19:306–319

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Lau NC, Lim LP, Weinstein EG et al (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862

    Article  CAS  PubMed  Google Scholar 

  20. Ghildiyal M, Seitz H, Horwich MD et al (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077–1081

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sarah E. Hall .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Ow, M.C., Lau, N.C., Hall, S.E. (2014). Small RNA Library Cloning Procedure for Deep Sequencing of Specific Endogenous siRNA Classes in Caenorhabditis elegans . In: Werner, A. (eds) Animal Endo-SiRNAs. Methods in Molecular Biology, vol 1173. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0931-5_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0931-5_6

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0930-8

  • Online ISBN: 978-1-4939-0931-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics