title: Cloning and expression of new microRNAs from zebrafish.
abstract: MicroRNAs (miRNAs) play an important role in development and regulate the expression of many animal genes by post-transcriptional gene silencing. Here we describe the cloning and expression of new miRNAs from zebrafish. By high-throughput sequencing of small-RNA cDNA libraries from 5-day-old zebrafish larvae and adult zebrafish brain we found 139 known miRNAs and 66 new miRNAs. For 65 known miRNAs and for 11 new miRNAs we also cloned the miRNA star sequence. We analyzed the temporal and spatial expression patterns for 35 new miRNAs and for 32 known miRNAs in the zebrafish by whole mount in situ hybridization and northern blotting. Overall, 23 of the 35 new miRNAs and 30 of the 32 known miRNAs could be detected. We found that most miRNAs were expressed during later stages of development. Some were expressed ubiquitously, but many of the miRNAs were expressed in a tissue-specific manner. Most newly discovered miRNAs have low expression levels and are less conserved in other vertebrate species. Our cloning and expression analysis indicates that most abundant and conserved miRNAs in zebrafish are now known.
authors.affiliation: Hubrecht Laboratory, Centre for Biomedical Genetics, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Wigard P
authors.initials: WP
authors.lastname: Kloosterman
authors.forename: Florian A
authors.initials: FA
authors.lastname: Steiner
authors.forename: Eugene
authors.initials: E
authors.lastname: Berezikov
authors.forename: Ewart
authors.initials: E
authors.lastname: de Bruijn
authors.forename: Jose
authors.initials: J
authors.lastname: van de Belt
authors.forename: Mark
authors.initials: M
authors.lastname: Verheul
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
authors.forename: Ronald H A
authors.initials: RH
authors.lastname: Plasterk
mesh_terms: D000818:Animals; D015152:Blotting, Northern; D003001:Cloning, Molecular; D015870:Gene Expression; D017403:In Situ Hybridization; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D015027:Zebrafish / Q000196:embryology / Q000235:genetics* / Q000254:growth & development
chemical_list: D035683:MicroRNAs