Conservation of gene architecture and domains amidst sequence divergence in the hsrpmega lncRNA gene across the Drosophila genus: An in silico analysiss

Abstract

The developmentally active and cell-stress responsive hsr{omega} locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame ORF{omega}, long stretch of unique tandem repeats and an overlapping mir-4951 near its 3 end. It produces multiple lncRNAs using two transcription start and four termination sites. Earlier studies revealed functional conservation in several Drosophila species but with little sequence conservation, in three experimentally examined species, of ORF{omega}, tandem repeat and other regions but ultra-conservation of 16nt at 5 and 60nt at 3 splice-junctions of the omega intron. Present bioinformatic study, using the splice-junction landmarks in Drosophila melanogaster hsr{omega}, identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries the short ORF{omega}, ultra-conserved splice junctions of omega intron, repeat region, conserved 3-end located mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in repeat sequences. Intriguingly, only the intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested in Chironomus and Ceratitis species. Amidst the high sequence divergence, the conserved organization of exons, ORF{omega} and omega intron in this genes proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsr{omega} lncRNAs and the small Omega peptide.