Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

Mohammed, J., Flynt, A. S., Panzarino, A. M., Mondal, M. M. H., DeCruz, M., Siepel, A., Lai, E. C. (January 2018) Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res, 28 (1). pp. 52-65. ISSN 1088-9051

URL: https://www.ncbi.nlm.nih.gov/pubmed/29233922
DOI: 10.1101/gr.226068.117

Abstract

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3' untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.

Item Type: Paper
Subjects: organism description > animal > insect > Drosophila
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: January 2018
Date Deposited: 20 Dec 2017 16:51
Last Modified: 26 Jan 2018 17:40
PMCID: PMC5749182
Related URLs:
URI: http://repository.cshl.edu/id/eprint/35732

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