title: Identification and characterization of 63 MicroRNAs in the Asian seabass Lates calcarifer.
abstract: BACKGROUND
  MicroRNAs (miRNAs) play an important role in the regulation of many fundamental biological processes. So far miRNAs have been only identified in a few fish species, although there are over 30,000 fish species living under different environmental conditions on the earth. Here, we described an approach to identify conserved miRNAs and characterized their expression patterns in different tissues for the first time in a food fish species Asian seabass (Lates calcarifer).
  
  
  RESULTS
  By combining a bioinformatics analysis with an approach of homolog-based PCR amplification and sequencing, 63 novel miRNAs belonging to 29 conserved miRNA families were identified. Of which, 59 miRNAs were conserved across 10-86 species (E value ≤ 10⁻⁴) and 4 miRNAs were conserved only in fish species. qRT-PCR analysis showed that miR-29, miR-103, miR-125 and several let-7 family members were strongly and ubiquitously expressed in all tissues tested. Interestingly, miR-1, miR-21, miR-183, miR-184 and miR-192 showed highly conserved tissue-specific expression patterns. Exposure of the Asian seabass to lipopolysaccharide (LPS) resulted in up-regulation of over 50% of the identified miRNAs in spleen suggesting the importance of the miRNAs in acute inflammatory immune responses.
  
  
  CONCLUSIONS
  The approach used in this study is highly effective for identification of conserved miRNAs. The identification of 63 miRNAs and determination of the spatial expression patterns of these miRNAs are valuable resources for further studies on post-transcriptional gene regulation in Asian seabass and other fish species. Further identification of the target genes of these miRNAs would shed new light on their regulatory roles of microRNAs in fish.
authors.affiliation: Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Republic of Singapore.
authors.forename: Jun Hong
authors.initials: JH
authors.lastname: Xia
authors.forename: Xiao Ping
authors.initials: XP
authors.lastname: He
authors.forename: Zhi Yi
authors.initials: ZY
authors.lastname: Bai
authors.forename: Gen Hua
authors.initials: GH
authors.lastname: Yue
mesh_terms: D000818:Animals; D001208:Asia; D001483:Base Sequence; D001492:Bass / Q000235:genetics* / Q000382:microbiology; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects; D007249:Inflammation / Q000235:genetics; D008070:Lipopolysaccharides / Q000494:pharmacology; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D014733:Vibrio / Q000187:drug effects
chemical_list: D008070:Lipopolysaccharides; D035683:MicroRNAs; D012322:RNA Precursors