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Oryza sativa RNA-dependent RNA polymerase 6 (OsRDR6) contributes to DSB formation in rice meiosis

ABSTRACT: Oryza sativa RNA-dependent RNA polymerase 6 (OsRDR6) contributes to DSB formation in rice meiosis

PROVIDER: PRJNA637566 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11933650.fastq.gz	Fastqsanger.gz
	SRR11933651.fastq.gz	Fastqsanger.gz
	SRR11933652.fastq.gz	Fastqsanger.gz
	SRR11933653.fastq.gz	Fastqsanger.gz
	SRR11933654.fastq.gz	Fastqsanger.gz

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Oryza sativa RNA-dependent RNA polymerase 6 (OsRDR6) contributes to DSB formation in rice meiosis

Project description:RNA-dependent RNA polymerase 6 (RDR6) is a core component of the small RNA biogenesis pathway, but its function in meiosis is unclear. Herein we report a new allele of OsRDR6 (Osrdr6-mei), which causes meiosis-specific phenotype in rice. In Osrdr6-mei, meiotic DSB formation was blocked to some extent. We further created a biallelic mutant, Osrdr6-bi, by crossing Osrdr6-mei with a knock out mutant, Osrdr6-edit (Osrdr6-edi). In Osrdr6-bi, 24 univalents were observed at diakinesis, and no histone H2AX phosphorylation (γH2AX) foci was detected in meiocytes, indicating that OsRDR6 is crucial for meiotic DSB formation. Compared with the wild type, the number of 21-nt small RNAs was dramatically reduced, while the number of 24-nt small RNAs was significantly increased in Osrdr6-mei. And thousands of DMRs discovered in Osrdr6-mei, implying that OsRDR6 plays an essential role on DNA methylation, especially CHH methylation. Meanwhile, the transcriptome data showed that 457 genes were down-regulated in the mutant; including three genes related to DSB formation: OsSDS, P31comet and CRC1. Interestingly, the increased 24-nt small RNA level surrounding down-regulated genes was largely associated with the silencing of these genes, while DMRs were rarely related to them. In summary, we speculated that the small RNA levels are disordered in Osrdr6 mutants, which may lead to the defection of DSB formation.

2021-06-05 | GSE151871 | GEO

RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis [RNA-Seq]

Project description:Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.

2023-12-18 | GSE228453 | GEO

RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis[PRO-Seq]

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Polymerase recycling contributes to transcriptional noise

Project description:Polymerase recycling contributes to transcriptional noise

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DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [RNA-seq]

Project description:Meiotic recombination is initiated from the SPORULATION 11 (SPO11)-triggered formation of double strand breaks (DSBs) that usually occur in open chromatin with active transcriptional features in many eukaryotes. However, gene transcription at meiotic DSB sites appears to be detrimental for repair, and the mechanisms for gene silencing at DSB sites are largely undefined, especially in plants. Here, we demonstrate that the largest DNA polymerase epsilon subunit POL2A interacts with SU(VAR)3-9 homologs SUVH2 and SUVH9. N-SIM (Structured Illumination Microscopy) observation shows that the colocalization of SUVH2 with meiotic DSB marker γ- H2AX is dependent on POL2A. RNA-seq of male meiocytes identifies that POL2A and SUVH2 jointly repress the expression of 865 genes, which have several known characteristics associated with meiotic DSB sites. Bisulfite-seq and small RNA-seq of male meiocytes support the idea that the silencing of these genes by POL2A and SUVH2/9 is likely independent of CHH methylation or 24-nt siRNA accumulation. Consequently, pol2a suvh2 suvh9 triple mutants have more severe defects in meiotic recombination and fertility compared with either pol2a or suvh2 suvh9. Taken together, our results not only identify a new epigenetic regulatory mechanism for gene silencing in male meiocytes, but also reveal new roles for DNA polymerase and SUVH2/9 beyond their classic functions in mitosis.

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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

Project description:RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

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PRDM9 methyltransferase is essential for meiotic DSB formation

Project description:The programmed formation of hundreds DNA double strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA binding specificity of its zinc finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9 binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA binding specificities, we reveal severalthe basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset are selected for DSB formation.

2018-02-09 | GSE108953 | GEO

Chromatin remodeler Fun30 promotes efficient DSB end resection and recombination during yeast meiosis

Project description:Chromatin remodeler Fun30 promotes efficient DSB end resection and recombination during yeast meiosis

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