Conservation of gene architecture and domains amidst sequence divergence in thehsrωlncRNA gene across theDrosophilagenus: Anin silicoanalysis

Abstract

AbstractThe developmentally active and cell-stress responsivehsrω locus inDrosophila melanogastercarries two exons, oneomegaintron, one short translatable open reading frame ORFω, long stretch of unique tandem repeats and an overlappingmir-4951near its 3’ end. It produces multiple lncRNAs using two transcription start and four termination sites. Earlier studies revealed functional conservation in severalDrosophilaspecies but with little sequence conservation, in three experimentally examined species, of ORFω, tandem repeat and other regions but ultra-conservation of 16nt at 5’ and 60nt at 3’ splice-junctions of theomegaintron. Present bioinformatic study, using the splice-junction landmarks inDrosophila melanogaster hsrω, identified orthologues in publicly available 34Drosophilaspecies genomes. Each orthologue carries the short ORFω, ultra-conserved splice junctions ofomegaintron, repeat region, conserved 3’-end locatedmir-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 inChironomusandCeratitisspecies. Amidst the high sequence divergence, the conserved organization of exons, ORFω andomegaintron in this gene’s proximal part and tandem repeats in distal part across theDrosophilagenus is remarkable and possibly reflects functional importance of higher order structure ofhsrω lncRNAs and the small Omega peptide.