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The impact of age,biogenesis, and genomic clustering on Drosophila microRNA evolution
Authors:Jaaved Mohammed  Alex S Flynt  Adam Siepel  Eric C Lai
Institution:1.Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;2.Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA;3.Sloan-Kettering Institute, Department of Developmental Biology, New York, New York 10065, USA
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.
Keywords:microRNA evolution  structure evolution  microRNA clusters  mirtrons  Drosophila
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