title: Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.
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.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
authors.forename: H Rosaria
authors.initials: HR
authors.lastname: Chiang
authors.forename: Lori W
authors.initials: LW
authors.lastname: Schoenfeld
authors.forename: J Graham
authors.initials: JG
authors.lastname: Ruby
authors.forename: Vincent C
authors.initials: VC
authors.lastname: Auyeung
authors.forename: Noah
authors.initials: N
authors.lastname: Spies
authors.forename: Daehyun
authors.initials: D
authors.lastname: Baek
authors.forename: Wendy K
authors.initials: WK
authors.lastname: Johnston
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Shujun
authors.initials: S
authors.lastname: Luo
authors.forename: Joshua E
authors.initials: JE
authors.lastname: Babiarz
authors.forename: Robert
authors.initials: R
authors.lastname: Blelloch
authors.forename: Gary P
authors.initials: GP
authors.lastname: Schroth
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
mesh_terms: D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling; D005796:Genes / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics; D051379:Mice; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D043244:Ribonuclease III