Unraveling mitochondrial piRNAs in mouse embryonic gonadal cells

Abstract

Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small noncoding RNAs (sncRNAs), miRNAs, and more recently, piRNAs, is providing new functional perspectives in germ cell development and differentiation. piRNAs (PIWI-interacting RNAs) are single-stranded sncRNAs of mostly about 20–35 nucleotides, generated from the processing of pre-piRNAs. We leverage next-generation sequencing data obtained from mouse primordial germ cells and somatic cells purified from early-differentiating embryonic ovaries and testis from 11.5 to 13.5 days postcoitum. Using bioinformatic tools, we elucidate (i) the origins of piRNAs as transcribed from mitochondrial DNA fragments inserted in the nucleus or from the mitochondrial genome; (ii) their levels of expression; and (iii) their potential roles, as well as their association with genomic regions encoding other sncRNAs (such as tRNAs and rRNAs) and the mitochondrial regulatory region (D-loop). Finally, our results suggest how nucleo-mitochondrial communication, both anterograde and retrograde signaling, may be mediated by mitochondria-associated piRNAs.

A landscape of mouse mitochondrial small non-coding RNAs

“…piRNAs are largely present in the mitochondria of testis, representing the most predominant population of small RNAs ( Fig 2 ); their finding into mitochondria of testis is consistent with bioinformatic analyses on smallRNAseq libraries from primordial germ cells and spermatozoa of male mice [ 21 , 41 ]. Surprisingly, here piRNAs were also detected in the mitochondria of the other tissues, representing a novelty in the current knowledge ( S1 Table ).…”

“…Mitochondria were purified as described in Material and Methods section, and smallRNA sequencing experiments were performed on extracted RNAs ( ; their finding into mitochondria of testis is consistent with bioinformatic analyses on smallRNAseq libraries from primordial germ cells and spermatozoa of male mice [21,41]. Surprisingly, here piRNAs were also detected in the mitochondria of the…”

“…Surprisingly, here piRNAs were also detected in the mitochondria of the other tissues, representing a novelty in the current knowledge ( S1 Table ). In fact, although their presence has been already described for different somatic tissues [ 42 ] and related to epigenetic reprogramming and gene expression regulation [ 3 , 43 ], piRNAs specifically located in mitochondria are only reported in mammalian cancer cells [ 22 , 44 ] and inferred by bioinformatic analyses on RNA extracted from the whole cell lysates derived from murine primordial germ cells, spermatozoa oocytes, zygotes and embryonic gonadal cells [ 21 , 41 ]. Two studies have demonstrated a role of the mitochondrial protein MitoPLD/Zucchini (mammalian/Drosophila homologues) in piRNA biogenesis and piRNA mediated silencing in mouse and fly germlines [ 45 , 46 ]; finally, PIWIL-1, a human homologue of the mouse MIWI protein, has been detected in the mitochondria of human cells [ 44 ] pointing for a mitochondrial role in the biogenesis of piRNAs.…”

“…bioinformatic analyses on RNA extracted from the whole cell lysates derived from murine primordial germ cells, spermatozoa oocytes, zygotes and embryonic gonadal cells [21,41]. Two studies have demonstrated a role of the mitochondrial protein MitoPLD/Zucchini (mammalian/Drosophila homologues) in piRNA biogenesis and piRNA mediated silencing in mouse and fly germlines [45,46]; finally, PIWIL-1, a human homologue of the mouse MIWI protein, has been detected in the mitochondria of human cells [44] pointing for a mitochondrial role in the biogenesis of piRNAs.…”

Mitochondrial Non-Coding RNAs Are Potential Mediators of Mitochondrial Homeostasis

“…Among these candidates, piR-mmu-7,456,245, which showed relatively high expression in all types of cells, was detected to localize in mitochondria [ 21 ]. This research group also identified piRNAs by RNA-seq, which might be generated from the mitochondrial genome—or mitochondrial counterparts in the nuclear genome in mouse embryonic gonadal cells—indicating a potential piRNA-mediated communication between mitochondria and the nucleus [ 22 ]. Overall, the research on mitochondrial piRNAs is still superficial.…”