Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

Abstract

Piwi-interacting RNAs (piRNAs) are Ϸ30 nucleotide noncoding RNAs that may be involved in transposon silencing in mammalian germline cells. Most piRNA sequences are found in a small number of genomic regions referred to as clusters, which range from 1 to hundreds of kilobases. We studied the evolution of 140 rodent piRNA clusters, 103 of which do not overlap protein-coding genes. Phylogenetic analysis revealed that 14 clusters were acquired after rat-mouse divergence and another 44 after rodent-primate divergence. Most clusters originated in a process analogous to the duplication of protein-coding genes by ectopic recombination, via insertions of long sequences that were mediated by flanking chromosome-specific repetitive elements (REs). Source sequences for such insertions are often located on the same chromosomes and also harbor clusters. The rate of piRNA cluster expansion is higher than that of any known gene family and, in contrast to other large gene families, there was not a single cluster loss. These observations suggest that piRNA cluster expansion is driven by positive selection, perhaps caused by the need to silence the ever-expanding repertoire of mammalian transposons.arms race ͉ molecular evolution ͉ small RNA ͉ positive selection E ukaryotic genomes contain a variety of small noncoding RNAs, including microRNAs (miRNAs), repeat-associated small interfering RNAs (rasiRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs). miRNAs regulate the expression of protein-coding genes, rasiRNAs are involved in transposon silencing, and siRNAs play a dual role in silencing genes and transposons (1). Because of a number of similarities between rasiRNAs in Drosophila and piRNAs in mammals, rasiRNAs are considered to be a subclass of piRNAs. Thus, mammalian piRNAs are hypothesized to also be involved in transposon silencing, although they may perform other functions as well (2). Some noncoding RNAs, in particular miRNAs, evolve very slowly (3). In contrast, small-scale evolution of piRNA sequences proceeds at a rate typical of nonfunctional genomic regions (4). Here, we consider the large-scale evolution of mammalian piRNA clusters. ResultsRecent Acquisition of Many piRNA Clusters. Thus far, 140 rat and mouse piRNA clusters have been described, each of which is most likely transcribed as a unit and subsequently processed into mature piRNAs (2, 4-8). We studied the evolution of each of these clusters within their genomic contexts (Table S1). For this purpose, we obtained regions that included 2 flanking protein-coding genes on either side of a cluster and constructed pairwise alignments of orthologous rat, mouse, human, dog, and cow regions. Thirty-seven clusters overlap protein-coding genes, often spanning several exons and introns. All of these clusters are ancestral, being present in rat, mouse, and human, which is not surprising because protein-coding genes are generally conserved. Among the remaining 103 clusters, each of which is contained within an intergenic region, only 43 are ancestr...

Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

“…Therefore, we now consider other possibilities, such as the duplication of the chr17 piRNA generating region in J1 ES cells: In this case, the homozyotes may be viable but misidentified as heterozygotes because of the existence of one extra copy of the wild-type region. This is consistent with the report that the rate of piRNA cluster expansion is higher than that of any known gene family (Assis and Kondrashov 2009). A more detailed study is now ongoing to resolve this issue.…”

Two modes of targeting transposable elements by piRNA pathway in human testis

“…Additionally, a sharp increase in the number of testis-specific lincRNAs is also seen in amniotes (Hezroni et al 2015). Therefore, constant evolutionary turnover of sets of testis-specific lincRNAs might be, at least in part, responsible for the definition of pachytene piRNA repertoires, reminiscent of piRNA cluster evolution in rodents (Assis and Kondrashov 2009). It is also noteworthy that transcription of many of these evolutionary young lincRNAs is driven by LTR elements both in humans and rodents (Kapusta et al 2013;Chen et al 2016).…”

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

“…It was recently demonstrated that microRNAs, a class of small RNAs that are generally conserved, stand as a dynamic class of genes in terms of birth and death at both the macro-and microevolutionary levels (Allen et al 2004;Fahlgren et al 2007;Grimson et al 2008;Lu et al 2008a,b). It was also found that the piRNAs are evolutionarily dynamic in rodents (Assis and Kondrashov 2009) as well as in Drosophila ). In Drosophila, transposition/retrotransposition and excision of TEs occur frequently, and TE insertions are highly polymorphic among individuals (Montgomery and Langley 1983;Charlesworth and Langley 1989;Nuzhdin 1999;Petrov et al 2003;Gonzalez et al 2008).…”