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Open Access Highly Accessed Research

Conserved microRNA editing in mammalian evolution, development and disease

Maria Warnefors12*, Angélica Liechti1, Jean Halbert1, Delphine Valloton1 and Henrik Kaessmann12

Author Affiliations

1 Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland

2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

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Genome Biology 2014, 15:R83  doi:10.1186/gb-2014-15-6-r83

Published: 25 June 2014

Abstract

Background

Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are known to be edited at identical positions in human and mouse, the evolution of miRNA editing has not been investigated in detail. In this study, we identify conserved miRNA editing events in a range of mammalian and non-mammalian species.

Results

We demonstrate deep conservation of several site-specific miRNA editing events, including two that date back to the common ancestor of mammals and bony fishes some 450 million years ago. We also find evidence of a recent expansion of an edited miRNA family in placental mammals and show that editing of these miRNAs is associated with changes in target mRNA expression during primate development and aging. While global patterns of miRNA editing tend to be conserved across species, we observe substantial variation in editing frequencies depending on tissue, age and disease state: editing is more frequent in neural tissues compared to heart, kidney and testis; in older compared to younger individuals; and in samples from healthy tissues compared to tumors, which together suggests that miRNA editing might be associated with a reduced rate of cell proliferation.

Conclusions

Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes. Furthermore, we find that although miRNA editing is rare compared to editing of long RNAs, miRNAs are greatly overrepresented among conserved editing targets.