The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

Mohammed, J., Flynt, A. S., Siepel, A., Lai, E. C. (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA, 19 (9). pp. 1295-308. ISSN 1355-8382

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URL: http://www.ncbi.nlm.nih.gov/pubmed/23882112
DOI: 10.1261/rna.039248.113

Abstract

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence Computational Biology Conserved Sequence Drosophila/*genetics/metabolism *Evolution, Molecular *Genome, Insect MicroRNAs/*genetics/metabolism Models, Genetic *Multigene Family Drosophila microRNA clusters microRNA evolution mirtrons structure evolution
Subjects: organism description > animal > insect > Drosophila
bioinformatics > computational biology
evolution
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 14 Jan 2015 16:52
Last Modified: 14 Jan 2015 16:52
PMCID: PMC3753935
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31085

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