Adaptive evolution of testis-specific, recently evolved, clustered miRNAs inDrosophila

Abstract

The propensity of animal miRNAs to regulate targets bearing modest complementarity, most notably via pairing with miRNA positions ∼2-8 (the "seed"), is believed to drive major aspects of miRNA evolution. First, minimal targeting requirements have allowed most conserved miRNAs to acquire large target cohorts, thus imposing strong selection on miRNAs to maintain their seed sequences. Second, the modest pairing needed for repression suggests that evolutionarily nascent miRNAs may generally induce net detrimental, rather than beneficial, regulatory effects. Hence, levels and activities of newly emerged miRNAs are expected to be limited to preserve the status quo of gene expression. In this study, we unexpectedly show that Drosophila testes specifically express a substantial miRNA population that contravenes these tenets. We find that multiple genomic clusters of testis-restricted miRNAs harbor recently evolved miRNAs, whose experimentally verified orthologs exhibit divergent sequences, even within seed regions. Moreover, this class of miRNAs exhibits higher expression and greater phenotypic capacities in transgenic misexpression assays than do non-testis-restricted miRNAs of similar evolutionary age. These observations suggest that these testis-restricted miRNAs may be evolving adaptively, and several methods of evolutionary analysis provide strong support for this notion. Consistent with this, proof-of-principle tests show that orthologous miRNAs with divergent seeds can distinguish target sensors in a species-cognate manner. Finally, we observe that testis-restricted miRNA clusters exhibit extraordinary dynamics of miRNA gene flux in other Drosophila species. Altogether, our findings reveal a surprising tissue-directed influence of miRNA evolution, involving a distinct mode of miRNA function connected to adaptive gene regulation in the testis.

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

“…Moreover, we draw attention to the completely divergent evolutionary behavior of generally somatic miRNA clusters with that of testis-restricted miRNA clusters, which we have shown to be both adaptive as well as prone to exceptionally high rates of de novo hairpin birth (Mohammed et al 2014). Such findings broadly extend the notion that miRNAs do not evolve at a universal rate, but instead exhibit distinct behavior and flux based on a variety of features.…”

“…Instead, the evidence supports that a majority of such miRNA clusters emerged by acquisition and neofunctionalization of extant miRNA copies located elsewhere in the genome. This contrasts with the behavior of testis-restricted Drosophilid miRNA clusters, which exhibit accelerated evolutionary dynamics, including adaptive behavior and a dominant trend for de novo hairpin birth (Mohammed et al 2014).…”

“…6C). Finally, there are numerous instances of clustered miRNAs that were exclusively born recently within individual Drosophila lineages, and these are predominantly restricted to the testis (Mohammed et al 2014). The accelerated evolutionary dynamics of testis-restricted miRNA clusters appears to represent a special scenario that may be linked to their adaptive evolution (Mohammed et al 2014).…”

“…On the other hand, many miRNAs annotated in D. melanogaster were born relatively recently during Drosophilid radiation (Berezikov et al 2010(Berezikov et al , 2011Mohammed et al 2013). A substantial number of these reside in testis-restricted genomic clusters that evolve according to adaptive dynamics that are not typical of bulk miRNA loci (Lyu et al 2014;Mohammed et al 2014). As we recently detailed the evolutionary properties of rapidly evolving testisrestricted miRNA clusters (Mohammed et al 2014), we focus here on those miRNA clusters whose members are well-conserved among the sequenced fruitflies (i.e., pan-Drosophilid miRNA clusters).…”

MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution

“…Since perfect pairing between the seed and a target site is crucial for target recognition (Bartel 2009), most studies have assumed that miRNAs with the same seeds target the same set of genes (Enright et al 2003;Stark et al 2003;John et al 2004;Rajewsky and Socci 2004;Brennecke et al 2005;Grün et al 2005;Lewis et al 2005;Friedman et al 2009;). Metazoan miRNAs are evolutionarily dynamic Fahlgren et al 2007;Zhang et al 2007Lu et al 2008a,b;Liang and Li 2009;Berezikov 2011;Mohammed et al 2013Mohammed et al , 2014aLyu et al 2014;Wang et al 2016), and the repertoire of functional miRNAs has gradually expanded during metazoan evolution (Hertel et al 2006;Wheeler et al 2009;Berezikov 2011). Duplication is an important mechanism for miRNA expansions.…”