title: Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.
abstract: We sequenced approximately 400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV-primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs).
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: J Graham
authors.initials: JG
authors.lastname: Ruby
authors.forename: Calvin
authors.initials: C
authors.lastname: Jan
authors.forename: Christopher
authors.initials: C
authors.lastname: Player
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
authors.forename: William
authors.initials: W
authors.lastname: Lee
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Hui
authors.initials: H
authors.lastname: Ge
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D017124:Conserved Sequence; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014529:Uridine / Q000378:metabolism
chemical_list: D029742:Caenorhabditis elegans Proteins; D035683:MicroRNAs; D018510:RNA, Helminth; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; D012324:RNA-Dependent RNA Polymerase; D014529:Uridine