In silico analysis of V-SINE superfamily distribution in the zebrafish genome.

All eukaryotic genomes contain mobile elements and their role in the shaping of eukaryotic genomes is becoming more and more recognized, although the proportion and activity of the different classes of these elements widely varies between genomes. We used an in silico approach to analyze the presence and distribution of one of this family, the V-SINE sequences, in Danio rerio chromosomes. V-SINEs is a superfamily of vertebrate short interspersed repetitive elements, whose central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be ~550 Myr old. The central conserved domain might have been subject to some form of positive selection. A total of 108625 V-SINEs fragments have been identified on the 25 assembled Danio rerio chromosomes (danrer6), accounting for about 0.019% of the entire sequence. The average number of V-SINEs fragments per chromosome is about 4372 (±943), ranging from 2628 to 6571. We estimated that about 20% (±3%) of V-SINES per chromosome were found to be located within genic sequences, the main contribution due to their presence in the introns. In particular, we found a striking bias of V-SINES localization in 5? UTRs with respect to the 3? ones. The 5?UTR/3? ratio was estimate to be about 6.73. Our results seem to confirm that V-SINEs preferentially accumulate within relatively gene-rich regions, as previously seen by their in situ mapping on chromosomes. Besides, since, in mice, evidences have already shown that SINEs located in 5?UTR can contribute to the repression of gene expression, we suggest that, in Danio, the biased distribution of V-SINES in the 5?UTR vs 3? UTR regions, could be a scratch of their potential role in gene regulation.