Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes II
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ABSTRACT:
PROVIDER: PRJNA1079814 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28074745_1.fastq.gz | Fastqsanger.gz | |||
| SRR28074745_2.fastq.gz | Fastqsanger.gz | |||
| SRR28074746_1.fastq.gz | Fastqsanger.gz | |||
| SRR28074746_2.fastq.gz | Fastqsanger.gz | |||
| SRR28074747_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes
| PRJNA824784 | ENA
Project description:We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.
2024-03-06 | GSE200470 | GEO
Project description:We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.
2024-03-06 | GSE256514 | GEO
Project description:BackgroundSmall RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs control transposable elements in mammalian oocytes.ResultsHere, we use high-throughput sequencing to profile small RNAs and poly(A)-bearing long RNAs in oocytes of 12 representative vertebrate species (including 11 mammals). The results show that miRNAs are generally expressed in the oocytes of each representative species (although at low levels), whereas endo-siRNAs are specific to mice. Notably, piRNAs are predominant in oocytes of all species (except mice) and vary widely in length. We find PIWIL3-associated piRNAs are widespread in mammals and generally lack 3'-2'-O-methylation. Additionally, sequence identity is low between homologous piRNAs in different species, even among those present in syntenic piRNA clusters. Despite the species-specific divergence, piRNAs retain the capacity to silence younger TE subfamilies in oocytes.ConclusionsCollectively, our findings illustrate a high level of diversity in the small RNA populations of mammalian oocytes. Furthermore, we identify sequence features related to conserved roles of small RNAs in silencing TEs, providing a large-scale reference for future in-depth study of small RNA functions in oocytes.
| S-EPMC10964541 | biostudies-literature
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:Oocytes must accumulate and store maternal factors such as proteins during growth to sustain the first stages of embryonic development. How mammalian oocytes store maternal proteins is not understood. Here, we show that mouse and human oocytes store proteins on cytoplasmic lattices. With super-resolution light microscopy and electron tomography, we demonstrate that cytoplasmic lattices are twisted filament bundles formed by proteins of the subcortical maternal complex, filling the entire ooplasm. The lattices were associated with many proteins that have crucial functions during early embryo development, including proteins controlling genome methylation. Loss of cytoplasmic lattices prevented the accumulation of these proteins and resulted in early embryonic arrest. Thus, cytoplasmic lattices are important for storage of essential maternal proteins and the developmental success of early mammalian embryos.
2023-10-23 | PXD038575 | Pride
Project description:We aim to comprehensively characterize the small RNA population in oocytes Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals. Keywords: small RNAs profile
2008-03-28 | GSE10364 | GEO
Project description:Mammalian oocytes store proteins in cytoplasmic lattices
| PRJNA923596 | ENA
Project description:RNA-directed transposon silencing operates in the mammalian soma and germline tosafeguard genomic integrity. The piRNA pathway and the HUSHcomplex identify activetransposons through recognition of their nascent transcripts, but mechanisticunderstanding of how these distinct pathways evolved is lacking. TASOR is anessential component of the HUSH complex. TASOR’s DUF3715 domain adopts apseudo-PARP structure and is required for transposon silencing in a mannerindependent of complex assembly. TEX15, an essential piRNA pathway factor, alsocontains the DUF3715 domain. Here, we show that TASOR’s and TEX15’s DUF3715domain share extensive structural homology. We found that the DUF3715 domain arosein early eukaryotes and that in vertebrates it is restricted to TEX15, TASOR, andTASORB orthologues. While TASOR-like proteins are found throughout metazoa,TEX15 is vertebrate specific. The branchingof TEX15 and TASOR-like DUF3715 domainlikely occurred in early metazoan evolution. Remarkably, despite this vast evolutionarydistance, the DUF3715 domain from divergent TEX15 sequences can functionallysubstitute for the same domain in TASOR and mediates transposon silencing. We havethus termed this domain of unknown function as the RNA-directed pseudo-PARPtransposon silencing (RDTS) domain. In summary, we show an unexpected functionallink between these critical transposon silencing pathways.
2023-10-26 | GSE234730 | GEO