Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate

Abstract

Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here, we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, although 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, unlike in mice, marmoset piRNA clusters are also found on the X chromosome, suggesting escape from meiotic sex chromosome inactivation by the X-linked clusters. Some of the piRNA clusters identified contain antisenseorientated pseudogenes, suggesting the possibility that pseudogene-derived piRNAs may regulate parental functional proteincoding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, may regulate protein-coding genes via pseudogene-derived piRNAs, and may even play roles in meiosis in the adult marmoset testis.

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

“…As in marmoset, we were able to find pachytene clusters that are transcribed divergently from a promoter region shared with a protein-coding gene (Hirano et al 2014): e.g., BUB1, WDR1 as in marmoset and a new instance with TDRD5, which was described neither in mouse nor in marmoset.…”

“…Notably, as in previous studies on human, marmoset, and mouse small RNAs (Hirano et al 2014;Rounge et al 2015;Kumar et al 2016;Sharma et al 2016), we observed the presence of 31-to 34-nt-long 5 ′ -tiRs (long 5 ′ fragments of tRNAs, Kumar et al 2016). Moreover, using modified bioinformatics pipeline (see Materials and Methods), we were able to detect nontemplated tailing of miRNAs, piRNAs, and 5 ′ -tiRs with different biases for tailed nucleotides and nucleotide combinations (Supplemental Tables S1B, S1B1 and Supplemental Fig.…”

“…Later in development, most postnatal piRNAs are produced from specific genomic regions termed piRNA clusters and divided into two types, depending on the stage of their expression: prepachytene clusters arising from genic sequences, and pachytene clusters of intergenic origin (Li et al 2013a). The details of both biogenesis and function of these two types of postnatal piRNAs in the developing testis remain unclear; however, several reports have proposed various hypotheses relating pachytene piRNAs to TE silencing or the control of gene expression in either an indiscriminate or targeted manner (Gou et al 2014;Hirano et al 2014;Goh et al 2015;Zhang et al 2015;Vourekas et al 2016).…”

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

“…Gene-derived piRNAs were studied in Drosophila, Xenopus, mice, pig and primates including human. [56][57][58][59] However, these studies identify protein-coding genes as piRNA targets computationally with little or without any experimental validation. In contrast, with the analysis of our degradome library we provide the first direct biochemical observation of the actual slicing of protein-coding gene transcripts and TEs mediated by piRNAs in a non-bilaterian animal.…”

piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis

“…This was true despite the fact that meiotic piRNA clusters were initially reported as being depleted of mobile element sequences as compared with the genome as a whole (Girard et al 2006). However, recent studies have shown that young, potentially active elements are enriched in meiotic piRNA clusters, and these show a bias in orientation such that antisense piRNAs are preferentially produced (Hirano et al 2014;KA Wasik, OH Tam, I Falciatori, SR Knott, M Hammell, VV Vagin, and GJ Hannon, in prep.). Despite strong evidence for LINEs as pachytene piRNA targets, it is unclear whether LINE activation is the root cause of the sterility of MIWI mutants.…”