Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
- H. Rosaria Chiang1,2,
- Lori W. Schoenfeld1,2,
- J. Graham Ruby1,2,7,
- Vincent C. Auyeung1,2,3,
- Noah Spies1,2,
- Daehyun Baek1,2,
- Wendy K. Johnston1,2,
- Carsten Russ4,
- Shujun Luo5,
- Joshua E. Babiarz6,
- Robert Blelloch6,
- Gary P. Schroth5,
- Chad Nusbaum4 and
- David P. Bartel1,2,8
- 1Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- 2Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- 3Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Cambridge, Massachustts 02139, USA;
- 4Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA;
- 5Illumina, Inc., Hayward, California 94545, USA;
- 6Institute for Regeneration Medicine, Center for Reproductive Sciences, and Department of Urology, University of California at San Francisco, San Francisco, California 94143, USA
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences confirmed 398 annotated miRNA genes and identified 108 novel miRNA genes. More than 150 previously annotated miRNAs and hundreds of candidates failed to yield sequenced RNAs with miRNA-like features. Ectopically expressing these previously proposed miRNA hairpins also did not yield small RNAs, whereas ectopically expressing the confirmed and newly identified hairpins usually did yield small RNAs with the classical miRNA features, including dependence on the Drosha endonuclease for processing. These experiments, which suggest that previous estimates of conserved mammalian miRNAs were inflated, provide a substantially revised list of confidently identified murine miRNAs from which to infer the general features of mammalian miRNAs. Our analyses also revealed new aspects of miRNA biogenesis and modification, including tissue-specific strand preferences, sequential Dicer cleavage of a metazoan precursor miRNA (pre-miRNA), consequential 5′ heterogeneity, newly identified instances of miRNA editing, and evidence for widespread pre-miRNA uridylation reminiscent of miRNA regulation by Lin28.
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Footnotes
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↵8 Corresponding author.
E-MAIL dbartel{at}wi.mit.edu; FAX (617) 258-6768.
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Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.1884710.
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Supplemental material is available at http://www.genesdev.org.
- Received November 11, 2009.
- Accepted March 19, 2010.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press