title: A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate.
abstract: MicroRNAs (miRNAs) have been implicated in various cellular processes. They are thought to function primarily as inhibitors of gene activity by attenuating translation or promoting mRNA degradation. A typical miRNA gene produces a predominant approximately 21-nucleotide (nt) RNA (the miRNA) along with a less abundant miRNA(*) product. We sought to identify miRNAs from the simple chordate Ciona intestinalis through comprehensive sequencing of small RNA libraries created from different developmental stages. Unexpectedly, half of the identified miRNA loci encode up to four distinct, stable small RNAs. The additional RNAs, miRNA-offset RNAs (moRs), are generated from sequences immediately adjacent to the predicted approximately 60-nt pre-miRNA. moRs seem to be produced by RNAse III-like processing, are approximately 20 nt long and, like miRNAs, are observed at specific developmental stages. We present evidence suggesting that the biogenesis of moRs results from an intrinsic property of the miRNA processing machinery in C. intestinalis.
authors.affiliation: Department of Molecular Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, California 94720-3200, USA.
authors.forename: Weiyang
authors.initials: W
authors.lastname: Shi
authors.forename: David
authors.initials: D
authors.lastname: Hendrix
authors.forename: Mike
authors.initials: M
authors.lastname: Levine
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haley
mesh_terms: D000818:Animals; D001483:Base Sequence; D053898:Biosynthetic Pathways; D002938:Ciona intestinalis / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated; D043244:Ribonuclease III