Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans

J. Graham Ruby, Calvin Jan, Christopher Player, Michael J. Axtell, William Lee, Chad Nusbaum, Hui Ge, David P. Bartel

Research output: Contribution to journalArticlepeer-review

756 Scopus citations


We sequenced ∼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).

Original languageEnglish (US)
Pages (from-to)1193-1207
Number of pages15
Issue number6
StatePublished - Dec 15 2006

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)


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