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Pleiotropic Constraints, Expression Level, and the Evolution of miRNA Sequences

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Abstract

Post-transcriptional gene regulation mediated by microRNAs (miRNAs) plays critical roles during development by modulating gene expression and conferring robustness to stochastic errors. Phylogenetic analyses suggest that miRNA acquisition could play a role in phenotypic innovation. Moreover, miRNA-induced regulation strongly impacts genome evolution, increasing selective constraints on 3′UTRs, protein sequences, and expression level divergence. Thus, it is essential to understand the factors governing sequence evolution for this important class of regulatory molecules. Investigation of the patterns of molecular evolution at miRNA loci have been limited in Caenorhabditis elegans because of the lack of a close outgroup. Instead, I used Caenorhabditis briggsae as the focus point of this study because of its close relationship to Caenorhabditis sp. 9. I also corroborated the patterns of sequence evolution in Caenorhabditis using published orthologous relationships among miRNAs in Drosophila. In nematodes and in flies, miRNA sequence divergence is not influenced by the genomic neighborhood (i.e., intronic or intergenic) but is nevertheless affected by the genomic context because X-linked miRNAs evolve faster than autosomal miRNAs. However, this effect of chromosomal linkage can be explained by differential expression levels rather than a fast-X effect. The results presented here support a universal negative relationship between rates of molecular evolution and expression level, and suggest that mutations in highly expressed miRNAs are more likely to be deleterious because they potentially affect a larger number of target genes. Finally, I show that many single family member miRNAs evolve faster than miRNAs from multigene families and have limited functional scope, suggesting that they are not strongly integrated in gene regulatory networks.

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Acknowledgments

I thank Asher Cutter for comments on the manuscript. I also thank the Associate Editor and one anonymous reviewer for valuable comments and suggestions. This work was supported by grants from the Ontario Ministry of Research and Innovation and the National Health Institutes (R01-GM096008).

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  1. Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada

    Richard Jovelin

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Jovelin, R. Pleiotropic Constraints, Expression Level, and the Evolution of miRNA Sequences. J Mol Evol 77, 206–220 (2013). https://doi.org/10.1007/s00239-013-9588-6

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