The developmental miRNA profiles of zebrafish as determined by small RNA cloning
- Po Yu Chen1,
- Heiko Manninga2,
- Krasimir Slanchev3,
- Minchen Chien4,
- James J. Russo4,
- Jingyue Ju4,5,
- Robert Sheridan6,
- Bino John6,
- Debora S. Marks7,
- Dimos Gaidatzis8,
- Chris Sander6,9,
- Mihaela Zavolan8,10, and
- Thomas Tuschl1,11
- 1Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10021, USA; 2Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany; 3Germ Cell Development, Max-Planck-Institute for Biophysical Chemistry, D-37070 Göttingen, Germany; 4Columbia Genome Center, New York, New York 10032, USA; 5Department of Chemical Engineering, Columbia University, New York, New York 10027, USA; 6Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA; 7Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; 8Biozentrum der Universität Basel, CH-4056 Basel, Switzerland
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).
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Footnotes
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Supplemental material is available at http://www.genesdev.org.
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Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.1310605.
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Corresponding authors.
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↵9 E-MAIL sander{at}mskcc.org; FAX (646) 735-0021.
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↵10 E-MAIL Mihaela.Zavolan{at}unibas.ch; FAX 41-61-267-15-84.
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↵11 E-MAIL ttuschl{at}mail.rockefeller.edu; FAX (212) 327-7652.
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- Accepted April 21, 2005.
- Received February 25, 2005.
- Cold Spring Harbor Laboratory Press
