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Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes

ABSTRACT: Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes

PROVIDER: PRJNA376426 | ENA |

REPOSITORIES: ENA

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Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes

Project description:Small RNAs have important functions. However, small RNAs in primate oocytes remain unexplored. Herein, we develop CAS-seq, a single-cell small RNA sequencing method, and profiled the small RNAs in human oocytes and embryos. We discover a class of ~20-nt small RNAs that are predominantly expressed in human and monkey oocytes, but not in mouse oocytes. They are specifically associated with HIWI3 (PIWIL3), whereas significantly shorter than the commonly known PIWI-interacting RNAs (piRNAs), designated as oocyte short piRNAs (os-piRNAs). Notably, the os-piRNAs in human oocytes lack 2’-O-methylation at the 3’ end, a hallmark of the classic piRNAs. In addition, the os-piRNAs have a strong 1U/10A bias and are enriched on the antisense strands of recently evolved transposable elements (TEs), indicating the potential function of silencing TEs by cleavage. Therefore, our study has identified an oocyte-specific piRNA family with distinct features and provides valuable resources for studying small RNAs in primate oocytes.

2019-06-13 | GSE95218 | GEO

Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes.

Project description: Not available

| S-EPMC6662892 | biostudies-literature

Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters

Project description:Many animals have a conserved adaptive genome defense system known as the Piwi-interacting RNA (piRNA) pathway which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes do not play a role in mammalian oocytes. Contrary to this, PIWIL1- and PIWIL3-defective golden hamsters we have produced show defects in production of functional oocytes. Mechanisms involved, however, vary between the two PIWI genes; lack of PIWIL1 has a strong impact on gene expression including hamster-specific young transposon de-silencing, while PIWIL3 deficiency has little impact on gene expression in oocytes, although DNA methylation of chromosomes was reduced to some extent. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes including humans, which cannot be possible with mice.

2021-07-02 | GSE164356 | GEO

Piwi proteins and piRNAs in mammalian oocytes and early embryos

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

Piwi proteins and piRNAs in mammalian oocytes and early embryos

2015-03-27 | GSE64942 | GEO

Decoding the 5’ nucleotide bias of PIWI-interacting RNAs (piRNAs)

Project description:Decoding the 5’ nucleotide bias of PIWI-interacting RNAs (piRNAs)

| PRJNA476241 | ENA

Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi

2009-09-01 | GSE15556 | GEO

Piwi proteins and piRNAs in mammalian oocytes and early embryos

Project description:Piwi proteins and piRNAs in mammalian oocytes and early embryos

| PRJNA272542 | ENA

PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function

Project description:PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function

| PRJNA362355 | ENA

Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi

Project description:Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Various small RNA libraries from single X.tropicalis eggs. Analysis of this series of files is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi". Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR and was sequenced with either the 454 Genome Sequencer FLX platform or the Illumina GA-II platform.

2009-08-31 | E-GEOD-15556 | biostudies-arrayexpress

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