title: The developmental miRNA profiles of zebrafish as determined by small RNA cloning.
abstract: MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).
authors.affiliation: Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10021, USA.
authors.forename: Po Yu
authors.initials: PY
authors.lastname: Chen
authors.forename: Heiko
authors.initials: H
authors.lastname: Manninga
authors.forename: Krasimir
authors.initials: K
authors.lastname: Slanchev
authors.forename: Minchen
authors.initials: M
authors.lastname: Chien
authors.forename: James J
authors.initials: JJ
authors.lastname: Russo
authors.forename: Jingyue
authors.initials: J
authors.lastname: Ju
authors.forename: Robert
authors.initials: R
authors.lastname: Sheridan
authors.forename: Bino
authors.initials: B
authors.lastname: John
authors.forename: Debora S
authors.initials: DS
authors.lastname: Marks
authors.forename: Dimos
authors.initials: D
authors.lastname: Gaidatzis
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D003001:Cloning, Molecular; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics*
chemical_list: D035683:MicroRNAs