Evolution of an X-linked primate-specific micro RNA cluster

Micro RNAs (miRNAs) are a class of small regulatory RNAs, which posttranscriptionally repress protein production of the targeted messenger RNAs (mRNAs). Accumulating evidence has suggested lineage-specific miRNAs have contributed to lineage-specific characteristics. However, the birth and death of these miRNAs, particularly in primates, largely remain unexplored. We herein characterized the evolutionary history of a newly discovered miRNA cluster on primate X-chromosome, spanning a approximately 33-kb region in human Xq27.3. The cluster consists of six distinct miRNAs, four of which are compactly organized in a 3-kb region belonging to a phylogenetic group distinct from the other two miRNAs. By comparing the genomic structure of this cluster in human with four other primates (chimpanzee, orangutan, rhesus macaque, and marmoset), we identified several previously uncovered miRNAs in these primates that share orthology with the human miRNAs. We found the entire miRNA cluster was well conserved among primate species but unidentifiable in other mammalian species (including mouse, rat, cat, dog, horse, cow, opossum, and platypus), suggesting that the formation of this cluster was after the primate-rodent split but before the emergence of New-World Monkey (represented by marmoset). Our analysis further revealed complex evolutionary dynamics on this locus, characterized by extensive duplication events. Phylogenetic analysis revealed birth and death of the miRNAs within this region, accompanied by rapid evolution, which highlighted their functional importance. These miRNAs are primarily expressed in primate epididymis, part of the male reproductive system. Our analysis showed that their predicted target mRNAs are significantly enriched for several functional classes relevant to epididymal physiology, such as morphogenesis of epithelium and tube development. Furthermore, several genes controlling sperm maturation and male fertility are confidently predicted to be their targets. Collectively, we argue these miRNAs might play an important role in epididymal morphogenesis and sperm maturation and in establishing primate-specific epididymal characteristics.