Advertisement

Computing siRNA and piRNA Overlap Signatures

  • Christophe AntoniewskiEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1173)

Abstract

High-throughput sequencing approaches opened the possibility to precisely map full populations of small RNAs to the genomic loci from which they originate. A bioinformatic approach revealed a strong tendency of sense and antisense piRNAs to overlap with each other over ten nucleotides and had a major role in understanding the mechanisms of piRNA biogenesis. Using similar approaches, it is possible to detect a tendency of sense and antisense siRNAs to overlap over 19 nucleotides. Thus, the so-called overlap signature which describes the tendency of small RNA to map in a specific way relative to each other has become the approach of choice to identify and characterize specific classes of small RNAs. Although simple in essence, the bioinformatic methods used for this approach are not easily accessible to biologists. Here we provide a python software that can be run on most of desktop or laptop computers to compute small RNA signatures from files of sequencing read alignments. Moreover, we describe and illustrate step by step two different algorithms at the core of the software and which were previously used in a number of works.

Keywords

High-throughput sequencing Small RNA signature siRNA piRNA 

References

  1. 1.
    Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC (2007) A slicer-mediated mechanism for repeat-associated siRNA 5’ end formation in Drosophila. Science 315:1587–1590PubMedCrossRefGoogle Scholar
  2. 2.
    Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089–1103Google Scholar
  3. 3.
    Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387–1392PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A et al (2009) The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138:1137–1149PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM et al (2009) Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137:509–521PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, Hannon GJ (2009) Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137:522–535PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Lau NC, Robine N, Martin R, Chung WJ, Niki Y, Berezikov E, Lai EC (2009) Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res 19:1776–1785PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    de Vanssay A, Bouge AL, Boivin A, Hermant C, Teysset L, Delmarre V, Antoniewski C, Ronsseray S (2012) Paramutation in Drosophila linked to emergence of a piRNA-producing locus. Nature 490:112–115PubMedCrossRefGoogle Scholar
  9. 9.
    Fagegaltier D, Bouge AL, Berry B, Poisot E, Sismeiro O, Coppee JY, Theodore L, Voinnet O, Antoniewski C (2009) The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A 106:21258–21263PubMedCentralPubMedCrossRefGoogle Scholar
  10. 10.
    van Mierlo JT, Bronkhorst AW, Overheul GJ, Sadanandan SA, Ekstrom JO, Heestermans M, Hultmark D, Antoniewski C, van Rij RP (2012) Convergent evolution of argonaute-2 slicer antagonism in two distinct insect RNA viruses. PLoS Pathog 8:e1002872PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Laboratoire de Biologie du Développement, Drosophila Genetics and EpigeneticsCNRS UMR 7622 and University Paris 6 Pierre et Marie CurieParis cedex 05France

Personalised recommendations