The developmental miRNA profiles of zebrafish as determined by small RNA cloning Journal Article
| Authors: | Chen, P. Y.; Manninga, H.; Slanchev, K.; Chien, M.; Russo, J. J.; Ju, J.; Sheridan, R.; John, B.; Marks, D. S.; Gaidatzis, D.; Sander, C.; Zavolan, M.; Tuschl, T. |
| Article 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 celltype-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). © 2005 by Cold Spring Harbor Laboratory Press. |
| Keywords: | controlled study; nonhuman; comparative study; animal cell; mammalia; animals; animal tissue; microrna; gene expression; embryo; cell line; prediction; animalia; molecular cloning; cloning, molecular; base sequence; development; transfer rna; micrornas; zebra fish; zebrafish; fibroblast culture; danio rerio; rna sequence; invertebrata; zygote; invertebrate; rasirna; blastula |
| Journal Title: | Genes and Development |
| Volume: | 19 |
| Issue: | 11 |
| ISSN: | 0890-9369 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2005-06-01 |
| Start Page: | 1288 |
| End Page: | 1293 |
| Language: | English |
| DOI: | 10.1101/gad.1310605 |
| PUBMED: | 15937218 |
| PROVIDER: | scopus |
| PMCID: | PMC1142552 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 125" - "Export Date: 24 October 2012" - "CODEN: GEDEE" - "Source: Scopus" |
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