Identification and Characterization of 63 MicroRNAs in the Asian Seabass Lates calcarifer

Abstract

BackgroundMicroRNAs (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).Methodology/Principal FindingsBy 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/SignificanceThe 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.

Characterization of Novel Precursor miRNAs Using Next Generation Sequencing and Prediction of miRNA Targets in Atlantic Halibut

“…2 and Dataset S2) is in agreement with reports showing pre-miRNA conservation in the two arms but allowing variation in the termini and the big loop regions [26], [27], [28]. Some of the identified precursors were similar to mammalian pre-miRNAs but have not been previously reported in teleosts.…”

“…For instance, Il-1β is expressed in various organs; Il-12β is highly expressed in immune related organs; and Il-6 exhibits more limited expression pattern and is primarily detected in thymus and brain [40]. Vibrio harveyi challenge experiment in Asian seabass ( Lates calcarifer ) has shown rapid transient elevated expression of both Il-1β and miR-21 in three immune related organs, indicating role of miRNAs in acute inflammatory immune responses [28]. In mammals, miRNAs are reported to target cytokine transcripts [41], [42].…”

“…5). miR-125 is abundantly expressed in brain of teleosts [28], [43]. In addition, kiss1r-2 , which is abundantly expressed in brain compared to gonad during Atlantic halibut maturation [44], is targeted by miR-34b and miR-574 (Table S1).…”

Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing

“…Moreover, a recent study on Nilaparvata lugens reported that miR-263a was found as high abundant miRNAs in the last instar female nymph females [78]. Both miR-8 and miR-184 were reported in the embryos of Drosophila [79, 80], mosquitoes [68, 81], silk worm [82], Schistosoma japonicum [83], zebrafish [84], Asian seabass[85], mouse [86–88] and humans [15, 89]. This suggest a conservative developmental function for these two miRNAs across different animals.…”

MicroRNA in Teleost Fish

“…Similarly, a number of miRNA species was identified in Asian seabass ( Lates calcarifer ) eye (Xia et al 2011). Spatial localization of miRNAs revealed cell type- and developmental stage-specific expression patterns (Kapsimali et al 2007).…”