CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors

Cell. 2012 Dec 21;151(7):1488-500. doi: 10.1016/j.cell.2012.11.023.


Piwi-interacting (pi) RNAs are germline-expressed small RNAs linked to epigenetic programming. C. elegans piRNAs are thought to be transcribed as independent gene-like loci. To test this idea and to identify potential transcription start (TS) sites for piRNA precursors, we developed CapSeq, an efficient enzymatic method for 5' anchored RNA profiling. Using CapSeq, we identify candidate TS sites, defined by 70-90 nt sequence tags, for >50% of annotated Pol II loci. Surprisingly, however, these CapSeq tags failed to identify the overwhelming majority of piRNA loci. Instead, we show that the likely piRNA precursors are ∼26 nt capped small (cs) RNAs that initiate precisely 2 nt upstream of mature piRNAs and that piRNA processing or stability requires a U at the csRNA +3 position. Finally, we identify a heretofore unrecognized class of piRNAs processed from csRNAs that are expressed at promoters genome wide, nearly doubling the number of piRNAs available for genome surveillance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / metabolism
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism
  • Gene Expression Profiling / methods*
  • Genome-Wide Association Study
  • Mice
  • Nucleotide Motifs
  • Promoter Regions, Genetic
  • RNA Caps / genetics*
  • RNA Polymerase II / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Helminth / genetics*
  • RNA, Small Interfering / genetics*
  • Transcription Initiation Site*


  • Argonaute Proteins
  • RNA Caps
  • RNA, Helminth
  • RNA, Small Interfering
  • RNA Polymerase II

Associated data

  • GEO/GSE40053