CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

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. [Display omitted] ► A new enzymatic method enriches 5′ ends of Pol II transcripts ► Identification of transcription start sites for most C. elegans Pol II genes ► Capped small RNAs of ∼26 nt are expressed from Pol II promoters genome wide ► csRNAs, but not longer capped RNAs, are the piRNA precursors in C. elegans A new method for genome-wide cloning of RNA polymerase II transcripts reveals capped 26-nucleotide RNAs as the elusive precursors for C. elegans piRNAs, which silence foreign nucleic acids.