Birth and expression evolution of mammalian microRNA genes

Abstract

MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup) with the aim to unravel the evolution of mammalian miRNAs. Our analyses reveal an overall expansion of miRNA repertoires in mammals, with threefold accelerated birth rates of miRNA families in placentals and marsupials, facilitated by the de novo emergence of miRNAs in host gene introns. Generally, our analyses suggest a high rate of miRNA family turnover in mammals with many newly emerged miRNA families being lost soon after their formation. Selectively preserved mammalian miRNA families gradually evolved higher expression levels, as well as altered mature sequences and target gene repertoires, and were apparently mainly recruited to exert regulatory functions in nervous tissues. However, miRNAs that originated on the X chromosome evolved high expression levels and potentially diverse functions during spermatogenesis, including meiosis, through selectively driven duplicationdivergence processes. Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces.

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

“…Before determining a novel miRNA's expression, we made sure to compensate for the sequence depth of the sample at hand: in particular, we used an adaptive thresholding strategy that required a miRNA to be supported by a higher number of sequence reads in samples that were more deeply sequenced. Generally, we found their average expression level to be somewhat lower than that of miRBase miRNAs, in agreement with previous reports (39,(54)(55)(56). We nonetheless stress that all of the novel miRNAs that we discovered are statistically significant (FDR ≤ 0.05) in at least one and typically in many of the analyzed samples: as a matter of fact, 91.5% of the newly discovered miRNAs are statistically significant in 10 or more of the processed samples.…”

“…Nonetheless, species-specific miRNAs (e.g., cel-lsy-6 in C. elegans) (62) have also been described and characterized as have been miRNAs that are present only in one or a few species of the same genus. Therefore, enforcing an organism-conservation requirement during miRNA searches is bound to limit the number of potential miRNAs that can be discovered, leaving organism-and lineage-specific miRNAs undiscovered (53)(54)(55)(56). In our effort to further characterize the human miRNA repertoire, we liberated ourselves from the conservation requirement: not surprisingly then, 56.7% of our newly discovered miRNAs are human-specific whereas 94.4% are primate-specific ( Table 2).…”

“…Many of the mature miRNA products that are contained in release 20 of miRBase are conserved among different genera: e.g., the well-conserved miRNA let-7. Several exceptions have also been reported, with the corresponding miRNAs being genus-specific (27,(53)(54)(55)(56). To determine the degree of conservation of our novel miRNAs, we performed a search where we sought instances not only of the mature miRNA but also of the full-length precursor (at two different thresholds) in several model organisms.…”

A critical appraisal of the use of microRNA data in phylogenetics

“…In all but the amniote study (19) (addressed below), secondary miRNA losses constitute between 27% and 54%, with an overall average of 38%, of the implied evolutionary changes. These phylogenetic results accord well with those of molecular evolutionary studies, in which prevalent secondary loss of miRNA families has been inferred for various taxa (14,(32)(33)(34)(35).…”

Cnidarian microRNAs frequently regulate targets by cleavage

“…We tested that these observations were robust to potential biases resulting from differences in miRNA annotation method and sequencing depth in the different species in two ways: first, by repeating the analysis using alternative miRNA sets for human (used for Fig. 4; Meunier et al 2013) and Nematostella miRNAs from miRBase 19 (not shown); and second, by partitioning our Nematostella miRNAs and the miRBase miRNAs by relative abundance level in each species (Supplemental Fig. S4).…”