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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sabin LR, Delas MJ, Hannon GJ (2013) Dogma derailed: the many influences of RNA on the genome. Mol Cell 49:783–794
Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108
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
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
Pak J, Fire A (2007) Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315:241–244
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
Pak J, Maniar JM, Mello CC et al (2012) Protection from feed-forward amplification in an amplified RNAi mechanism. Cell 151:885–899
Boisvert ME, Simard MJ (2008) RNAi pathway in C. elegans: the argonautes and collaborators. Curr Top Microbiol Immunol 320:21–36
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
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
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
Burkhart KB, Guang S, Buckley BA et al (2011) Pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation. PLoS Genet 7:e1002249
Guang S, Bochner AF, Pavelec DM et al (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321:537–541
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
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
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
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
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
Ghildiyal M, Seitz H, Horwich MD et al (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077–1081
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights 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