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Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: an in silico analysis

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Abstract

The developmentally active and cell-stress responsive hsrω locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame (ORFω), long stretch of unique tandem repeats and an overlapping mir-4951 near its 3′ end. It produces multiple long noncoding RNAs (lncRNAs) using two transcription start and four termination sites. Earlier cytogenetic studies revealed functional conservation of hsrω in several Drosophila species. However, sequence analysis in three species showed poor conservation for ORFω, tandem repeat and other regions while the 16 nt at 5′ and 60 nt at 3′ splice junctions of the omega intron, respectively, were found to be ultra-conserved. The present bioinformatic study using the splice-junction landmarks in D. melanogaster hsrω identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries a short ORFω, ultra-conserved splice junctions of omega intron, repeat region, conserved 3′-end located at mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in the repeat sequences. Intriguingly, only the omega 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 genera. Amidst the high sequence divergence, the conserved organization of exons, ORFω and omega intron in this gene’s proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsrω lncRNAs and the small omega peptide.

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Acknowledgements

We thank the Department of Biotechnology, Ministry of Science and Technology, Govt. of India, New Delhi for supporting this work (BT/PR6150/COE/34/20/2013). SCL is currently supported by the Science and Engineering Research Board (SERB), Govt. of India, as SERB Distinguished Fellow. RKS is supported by the Council of Scientific and Industrial Research, New Delhi through research fellowship. EM was supported by Summer Project fellowship of the Science Academies.

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  1. Eshita Mutt

    Present address: Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland

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  1. Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221 005, India

    Ranjan Kumar Sahu & Subhash Chandra Lakhotia

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Corresponding editor: H. A. Ranganath

RKS, EM and SCL undertook the bioinformatic analyses and wrote the manuscript.

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Sahu, R.K., Mutt, E. & Lakhotia, S.C. Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: an in silico analysis. J Genet 99, 64 (2020). https://doi.org/10.1007/s12041-020-01218-6

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