Analysis of redundancy between RNAi and piRNA pathways in the mouse oocytes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA545983 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10270021.fastq.gz | Fastqsanger.gz | |||
| SRR10270022.fastq.gz | Fastqsanger.gz | |||
| SRR10270023.fastq.gz | Fastqsanger.gz | |||
| SRR10270024.fastq.gz | Fastqsanger.gz | |||
| SRR10270025.fastq.gz | Fastqsanger.gz |
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Project description:Suppression of retrotransposons is an integral part of germline genome defense. The PIWI-associated RNA (piRNA) pathway mediates post-transcriptional and transcriptional silencing of retrotransposons in vertebrates. The loss of the piRNA pathway in mice results in male sterility while females remain fertile. Unlike spermatogenic cells, mouse oocytes utilize also RNA interference (RNAi) pathway, another small RNA pathway capable of retrotransposon suppression. To examine redundancy of piRNA and RNAi pathway in the mouse female germline, we produced an RNAi pathway mutant DicerSOM and crossed it with a catalytically-dead mutant of Mili, an essential piRNA factor. Ovaries and follicular development in mice lacking both pathways appear normal suggesting that RNAi in oocytes does not rescue a piRNA pathway knock-out phenotype. We observed that one of the pathways dominates in suppression of different retrotransposons. Intracisternal A Particle retrotransposon is mainly targeted by the piRNA pathway, MT and RLTR10 retrotransposons were targeted mainly by RNAi. Importantly, both pathways redundantly suppress LINE-1 retrotransposons where the loss of both RNA silencing pathways yielded ~6-fold upregulation of negligible levels of LINE-1 transcripts. This implies that another transcriptional silencing mechanism must contribute to LINE-1 repression and could explain why both, RNAi and piRNA pathways, are non-essential defense pathway in the mouse female germline.
2019-11-22 | GSE132121 | GEO
Project description:Germline genome defense evolves to recognize and suppress retrotransposons. One of defensive mechanisms is the PIWI-associated RNA (piRNA) pathway, which employs small RNAs for sequence-specific repression. The loss of the piRNA pathway in mice causes male sterility while females remain fertile. Unlike spermatogenic cells, mouse oocytes posses also RNA interference (RNAi), another small RNA pathway capable of retrotransposon suppression. To examine whether RNAi compensates the loss of the piRNA pathway, we produced a new RNAi pathway mutant DicerSOM and crossed it with a catalytically-dead mutant of Mili, an essential piRNA gene. Normal follicular and oocyte development in double mutants showed that RNAi does not suppress a strong ovarian piRNA knock-out phenotype. However, we observed redundant and non-redundant targeting of specific retrotransposon families illustrating stochasticity of recognition and targeting of invading retrotransposons. Intracisternal A Particle retrotransposon was mainly targeted by the piRNA pathway, MaLR and RLTR10 retrotransposons were targeted mainly by RNAi. Double mutants showed accumulations of LINE-1 retrotransposon transcripts. However, we did not find strong evidence for transcriptional activation and mobilization of retrotransposition competent LINE-1 elements suggesting that while both defense pathways are simultaneously expendable for ovarian oocyte development, yet another transcriptional silencing mechanism prevents mobilization of LINE-1 elements.
| S-EPMC6944382 | biostudies-literature
Project description:Mammals have one Dicer gene required for biogenesis of small RNAs in microRNA (miRNA) and RNA interference (RNAi) pathways. Yet, endogenous RNAi is highly active in oocytes but not in somatic cells. Here, we provide a mechanistical explanation for high RNAi activity in mouse oocytes. The main Dicer isoform in oocytes is transcribed from an intronic MT-C retrotransposon, which functions as a promoter of an oocyte-specific Dicer isoform (denoted DicerO). DicerO lacks an N-terminal helicase domain and has a higher cleavage activity than the full-length Dicer from somatic cells. DicerO can rescue the miRNA pathway and, in addition, it efficiently produces small RNAs from long dsRNA substrates. Thus, control of endogenous RNAi activity in mice occurs via alternative Dicer isoform and the phylogenetic origin of DicerO demonstrates evolutionary plasticity of RNA silencing pathways.
2013-11-07 | GSE41207 | GEO
Project description:Mammals have one Dicer gene required for biogenesis of small RNAs in microRNA (miRNA) and RNA interference (RNAi) pathways. Yet, endogenous RNAi is highly active in oocytes but not in somatic cells. Here, we provide a mechanistical explanation for high RNAi activity in mouse oocytes. The main Dicer isoform in oocytes is transcribed from an intronic MT-C retrotransposon, which functions as a promoter of an oocyte-specific Dicer isoform (denoted DicerO). DicerO lacks an N-terminal helicase domain and has a higher cleavage activity than the full-length Dicer from somatic cells. DicerO can rescue the miRNA pathway and, in addition, it efficiently produces small RNAs from long dsRNA substrates. Thus, control of endogenous RNAi activity in mice occurs via alternative Dicer isoform and the phylogenetic origin of DicerO demonstrates evolutionary plasticity of RNA silencing pathways. NIH3T3 cells or mouse embryonic stem cells expressing oocyte-specific or somatic form of Dicer were transiently transfected with a plasmid expressing long double-stranded RNA (within the 3'-UTR of EGFP reporter) or left without transfection for controls.
2013-11-07 | E-GEOD-41207 | biostudies-arrayexpress
Project description:Germ cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi-piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, while those in bovine ovary just express PIWIL1. In human, macaque and bovine ovaries we find piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative proteome analysis we show that these maturing oocytes strongly and specifically express the thus-far uncharacterized PIWIL3 protein, alongside other known piRNA-pathway components. In bovine early embryos these piRNAs are still abundant, revealing a potential impact of piRNAs on mammalian embryogenesis. Our results reveal unexpected, highly dynamic piRNA pathways in mammalian oocytes and early embryos. Analyses of multiple small RNA libraries obtained from fetal/adult oocytes, cumulus cells, ovary, testis and 2-4 cell stage ivf embryos of multiple mammalian species.
2015-03-27 | E-GEOD-64942 | biostudies-arrayexpress
Project description:Germ cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi-piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, while those in bovine ovary just express PIWIL1. In human, macaque and bovine ovaries we find piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative proteome analysis we show that these maturing oocytes strongly and specifically express the thus-far uncharacterized PIWIL3 protein, alongside other known piRNA-pathway components. In bovine early embryos these piRNAs are still abundant, revealing a potential impact of piRNAs on mammalian embryogenesis. Our results reveal unexpected, highly dynamic piRNA pathways in mammalian oocytes and early embryos.
2015-03-27 | GSE64942 | GEO
Project description:piRNA pathway is essential for generating functional oocytes in golden hamster
| PRJNA716965 | ENA
Project description:The animal piRNA pathway is a small RNA silencing system that acts in gonads and protects the genome against the deleterious influence of transposons. A major bottleneck in the field is the lack of comprehensive knowledge of the factors and molecular processes that constitute this pathway. We conducted an RNAi screen in Drosophila and identified ~50 genes that strongly impact the ovarian somatic piRNA pathway. Many identified genes fall into functional categories that indicate essential roles for mitochondrial metabolism, RNA export, the nuclear pore, transcription elongation and chromatin regulation in the pathway. Follow-up studies on two factors demonstrate the identification of components acting at distinct hierarchical levels of the pathway. Finally, we define CG2183/Gasz as a novel primary piRNA biogenesis factor in somatic and germline cells. Based on the similarities between insect and vertebrate piRNA pathways our results have far-reaching implications for the understanding of this conserved genome defense system. Steady-state RNA levels in wild-type ovarian somatic cells (OSC) and RNAi knock-downs of the piRNA pathway components.
2013-05-10 | E-GEOD-45894 | biostudies-arrayexpress
Project description:A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and novel components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. We identified and validated 87 genes necessary for transposon silencing. Among these were several novel piRNA biogenesis factors. We also found CG3893 (asterix) to be essential for transposon silencing, most likely by contributing to the effector step of transcriptional repression. Asterix loss leads to decreases in H3K9me3 marks on certain transposons but has no effect on piRNA levels.
2013-05-09 | GSE46009 | GEO
Project description:Here, we analyzed nine Drosophila piRNA pathway mutants for their impacts on both small RNA populations and the sub-cellular localization patterns of Piwi proteins. We find that distinct piRNA pathways with differing components function in ovarian germ and somatic cells. Keywords: Epigenetics
2009-04-30 | GSE15186 | GEO