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Crossovers from B6xCAST F1 PRDM9-Humanized/CAST testes

ABSTRACT: Crossovers from B6xCAST F1 PRDM9-Humanized/CAST testes

PROVIDER: PRJNA515881 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR8454660_1.fastq.gz	Fastqsanger.gz
	SRR8454660_2.fastq.gz	Fastqsanger.gz
	SRR8454670_1.fastq.gz	Fastqsanger.gz
	SRR8454670_2.fastq.gz	Fastqsanger.gz

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B6xCAST F1 PRDM9-Humanized/CAST testes

Project description:B6xCAST F1 PRDM9-Humanized/CAST testes

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Crossovers from B6xCAST F1 PRDM9-Humanized/CAST testes

Project description:We report 2,649 crossover breakpoints identified by single-cell DNA sequencing of 217 sperm in a B6xCAST F1 mouse, which is heterozygous at Prdm9, with one wild-type CAST allele and one allele found in human populations (bred from a genetically engineered mother, Davies et al Nature 2012). Separately, we have reported testis DMC1 enrichment in the same mouse (GSE124991). We also infer H3K4me3 intensities at DMC1 hotspots, based on the raw H3K4me3 ChIP-seq data published under GSE119727 (Li et al). We identify several factors, including PRDM9 binding on the repair-template homologue, telomere proximity and local GC-content, that affect the probability that a DSB is repaired as a crossover. We further show that these factors also influence the time it takes for the site of a DSB to find and engage its homologue, with rapidly-engaging sites being more likely to be repaired as crossovers.

2019-03-18 | GSE125326 | GEO

DMC1 ChIP-seq from B6xCAST F1 PRDM9-Humanized/CAST testes

Project description:We report testis DMC1 enrichment at DSB (Double-Strand Break) hotspots in a B6xCAST F1 mouse, which is heterozygous at Prdm9, with one wild-type CAST allele and one allele found in human populations (bred from genetically engineered mother, Davies et al Nature 2012). We also report H3K4me3 intensities at these hotspots, based on the raw data published under GSE119727 (Li et al). Separately, we have reported 2,649 crossover locations identified by single-cell DNA sequencing of 217 sperm from the same hybrid mouse. We identify several factors, including PRDM9 binding on the repair-template homologue, telomere proximity and local GC-content, that affect the probability that a DSB is repaired as a crossover. We further show that these factors also influence the time it takes for the site of a DSB to find and engage its homologue, with rapidly-engaging sites being more likely to be repaired as crossovers.

2019-03-18 | GSE124991 | GEO

H3K4me3 ChIP-seq from B6CASTF1-PRDM9 Humanized/CAST testes

Project description:We report testis H3K4me3 enrichment in an F1 male from a C57BL/6J (B6) x CAST/Eij (CAST) cross (B6 mother, CAST father). This mouse is heterozygous at PRDM9 for a humanized allele (Davies et al. Nature 2016) and the CAST allele. After filtering of promoter H3K4me3 regions, these data serve as a measure of PRDM9 binding enrichment on each homologue. We found that both crossovers and non-crossovers (observed by sequencing F2/F4/F5 genomic DNA) are depleted at "asymmetric" Double-Strand Break hotspots where PRDM9 primarily binds only one of the two homologues. This proves that PRDM9 plays an important role in promoting inter-homologue interactions and can explain why increasing PRDM9 binding asymmetry predicts hybrid infertility. See Li, Bitoun, Altemose et al. 2018 (pending) for a complete summary.

2018-09-28 | GSE119727 | GEO

DMC1 ChIP-seq from B6xCAST F1 PRDM9-Humanized/CAST testes

Project description:DMC1 ChIP-seq from B6xCAST F1 PRDM9-Humanized/CAST testes

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RPA and RAD51 ChIP-seq from B6 and B6xCAST F1 PRDM9-Humanized/CAST mouse testes

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RPA and RAD51 ChIP-seq from genetically modified Dmc1-knockout B6xCAST PRDM9-Humanized/CAST mouse testes

Project description:RPA and RAD51 ChIP-seq from genetically modified Dmc1-knockout B6xCAST PRDM9-Humanized/CAST mouse testes

| PRJNA1001892 | ENA

H3K4me3 ChIP-seq from B6CASTF1-PRDM9 Humanized/CAST testes

Project description:H3K4me3 ChIP-seq from B6CASTF1-PRDM9 Humanized/CAST testes

| PRJNA490145 | ENA

B6xCAST F1 PRDM9-Humanized/CAST testes

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-18 | GSE125327 | GEO

RPA and RAD51 ChIP-seq from B6 and B6xCAST F1 PRDM9-Humanized/CAST mouse testes

Project description:Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) and proceeds via binding of RPA, RAD51 and DMC1 to single-stranded DNA (ssDNA) substrates created after the formation of DSBs. Here, we report high-resolution in vivo maps of RPA and RAD51 binding in meiosis, mapping their binding locations and lifespans in a B6 and a genetically modified B6xCAST F1 mouse. We ascribe signals separately to the individual homologous chromosomes in the hybrid mouse, thereby separating the signal of binding to the chromosome where DSBs occurred and the chromosome that was used as template for repair. Together with super-resolution microscopy and DMC1 binding maps, we show that DMC1 and RAD51 have distinct spatial localization on ssDNA: whereas DMC1 binds near the break-site, RAD51 binds away from it. We characterize the D-loop, a critical intermediate bound by RPA, in vivo. These data show that DMC1, not RAD51, performs strand exchange in mammalian meiosis. We find that the localisation of D-loop intermediates is similar in crossover and non-crossover pathways, with a longer lifespan for crossover-destined intermediates. These findings answer long-standing questions about the molecular intermediates of recombination.

2020-06-30 | GSE143582 | GEO

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