TY - JOUR
T1 - Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans
AU - Ruby, J. Graham
AU - Jan, Calvin
AU - Player, Christopher
AU - Axtell, Michael J.
AU - Lee, William
AU - Nusbaum, Chad
AU - Ge, Hui
AU - Bartel, David P.
N1 - Funding Information:
We thank W. Johnston for assistance in preparing DNA for high-throughput sequencing, W. Brockman and P. Alvarez for base calling of sequencing run #1, and C. Perbost and others at 454 Life Sciences for sequencing runs #2–5, and J. Pak and A. Fire for sharing sequencing data before publication. We also thank S. Bagby, A. Grishok, A. Grimson, A. Mallory, and H. Vaucheret for useful comments on the manuscript. The SAGE data were produced at the Michael Smith Genome Sciences Centre with funding from Genome Canada. Our work was supported by the Prix Louis D from the Institut de France and a grant from the NIH (D.P.B). D.P.B is an HHMI Investigator.
PY - 2006/12/15
Y1 - 2006/12/15
N2 - 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).
AB - 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).
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U2 - 10.1016/j.cell.2006.10.040
DO - 10.1016/j.cell.2006.10.040
M3 - Article
C2 - 17174894
AN - SCOPUS:33845436047
SN - 0092-8674
VL - 127
SP - 1193
EP - 1207
JO - Cell
JF - Cell
IS - 6
ER -