PUBLICATION
Genomic Organization of Zebrafish microRNAs
- Authors
- Thatcher, E.J., Bond, J.M., Paydar, I., and Patton, J.G.
- ID
- ZDB-PUB-080602-15
- Date
- 2008
- Source
- BMC Genomics 9: 253 (Journal)
- Registered Authors
- Patton, James G., Thatcher, Elizabeth
- Keywords
- none
- MeSH Terms
-
- Animals
- Chromosomes/genetics
- Genome/genetics
- Genomic Library
- Genomics*
- Humans
- Mice
- MicroRNAs/genetics*
- Transcription, Genetic
- Zebrafish/genetics*
- PubMed
- 18510755 Full text @ BMC Genomics
Citation
Thatcher, E.J., Bond, J.M., Paydar, I., and Patton, J.G. (2008) Genomic Organization of Zebrafish microRNAs. BMC Genomics. 9:253.
Abstract
BACKGROUND: microRNAs (miRNAs) are small (~22 nt) non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. RESULTS: We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. CONCLUSIONS: Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family) contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping