Principles of chromosome organization for meiotic recombination
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE262343 | GEO | 2024/04/23
REPOSITORIES: GEO
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Project description:During mouse meiosis, DNA double-strand breaks (DSBs) are initiated by SPO11 at recombination hotspots (HSs), activated by PRDM9. Although activated HSs are marked by H3K4me3 and H3K36me3 histone modifications at open chromatin, most of the DSB-initiating and repair proteins are associated with the chromosome axis. This study addresses the mechanistic importance of the axis-associated cohesin proteins in DSB formation. We demonstrate that interactions between PRDM9 and the meiotic axis proteins STAG3 and REC8 are essential for efficient DSB formation. The absence of STAG3 or REC8 leads to inefficient meiotic DSB formation at HSs. STAG3 is critical for DSB formation, even at PRDM9-independent DSB-sites. Also, STAG3 and REC8 facilitate recruitment of the DSB-promoting proteins HORMAD1, IHO1 and MEI4 required for SPO11 activity. Together, these results support an evolutionarily conserved model in which axis-associated cohesin complexes recruit recombination-initiating proteins to DSB sites to promote meiotic recombination initiation.
2019-03-07 | GSE112110 | GEO
Project description:Recombination-mediated linking of homologous chromosomes is a unique meiotic feature that enables the halving of chromosomal ploidy in sexual life cycles. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) that are generated by focal multi-protein clusters that condense onto chromosomal axes by poorly understood mechanisms. We discovered in mice that a DBF4-dependent kinase (DDK)–modulated interaction between IHO1 and the chromosomal axis component HORMAD1 effects the formation of axis-bound IHO1 platforms that enhance nucleation of cytologically distinguishable DSB-machinery clusters. This IHO1-HORMAD1-mediated seeding of the DSB-machinery ensures that sufficient DSBs form for efficient pairing of homologous chromosomes. In the absence of IHO1-HORMAD1 interaction, residual DSB activity depends on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, meiotic DSBs are ensured by complementing pathways that differentially effect seeding and growth of DSB-machinery clusters, and that synergistically enable assembly of the DSB machinery on chromosomal axes.
2024-02-23 | PXD042221 | Pride
Project description:Recombination-mediated linking of homologous chromosomes is a unique meiotic feature that enables the halving of chromosomal ploidy in sexual life cycles. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) that are generated by focal multi-protein clusters that condense onto chromosomal axes by poorly understood mechanisms. We discovered in mice that a DBF4-dependent kinase (DDK)–modulated interaction between IHO1 and the chromosomal axis component HORMAD1 effects the formation of axis-bound IHO1 platforms that enhance nucleation of cytologically distinguishable DSB-machinery clusters. This IHO1-HORMAD1-mediated seeding of the DSB-machinery ensures that sufficient DSBs form for efficient pairing of homologous chromosomes. In the absence of IHO1-HORMAD1 interaction, residual DSB activity depends on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, meiotic DSBs are ensured by complementing pathways that differentially effect seeding and growth of DSB-machinery clusters, and that synergistically enable assembly of the DSB machinery on chromosomal axes.
2024-02-23 | PXD042179 | Pride
Project description:Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.
2020-11-19 | GSE145768 | GEO
Project description:PRDM9 specifies the sites of meiotic DNA double strand break that initiate meiotic recombination in mice and humans. PRDM9 is known to bind to specific DNA sequences with its DNA binding domain, to induce H3K4me3 and H3K36me3 to adjacent nucleosomes through its methyltransferase activity, and to recruit or activate the meiotic DSB machinery. To understand how PRDM9 executes these various steps, we set up to identify its partners. This was performed by a proteomic approach where protein extracts from mouse testis were immunoprecipitated with anti-PRDM9 antibody for mass spectrometry analysis.
2020-12-03 | PXD017337 | Pride
Project description:Meiotic chromosome architecture called M-bM-^@M-^\axis-loop structuresM-bM-^@M-^] and histone modifications have been demonstrated to regulate the Spo11-dependent formation of DNA double-strand breaks (DSBs) that trigger meiotic recombination. Using genome-wide chromatin immunoprecipitation (ChIP) analyses followed by deep sequencing, we compared the genome-wide distribution of the axis protein Rec8 (the kleisin subunit of meiotic cohesin) with that of oligomeric DNA covalently bound to Spo11, indicative of DSB sites. The frequency of DSB sites is overall constant between Rec8 binding sites. However, DSB cold spots are observed in regions spanning M-BM-10.8 kb around Rec8 binding sites. The axis-associated cold spots are not due to exclusion of Spo11 localization from the axis, since ChIP experiments revealed that substantial Spo11 persists at Rec8 binding sites during DSB formation. Spo11 fused with Gal4 DNA binding domain (Gal4BD-Spo11) tethered in close proximity (M-bM-^IM-$0.8 kb) to Rec8 binding sites hardly forms meiotic DSBs, in contrast with other regions. In addition, H3K4 tri-methylation (H3K4me3) remarkably decreases at Rec8 binding sites. These results suggest that reduced histone H3K4me3 in combination with inactivation of Spo11 activity on the axis discourages DSB hot spot formation. ChIP-chip analysis of Rec8 on fission yeast meiotic chromosomes
2014-03-31 | E-GEOD-52858 | biostudies-arrayexpress
Project description:In most mammals, including mice and humans, meiotic recombination is determined by the meiosis specific histone methytransferase PRDM9, which binds to specific DNA sequences and trimethylates histone 3 at lysine-4 and lysine-36 at the adjacent nucleosomes. These actions ensure successful DNA double strand break formation and repair that occur on the proteinaceous structure forming the chromosome axis. The process of hotspot association with the axis after their activation by PRDM9 is poorly understood. Previously, we and others have identified CXXC1, an ortholog of S. cerevisiae Spp1 in mammals, as a PRDM9 interactor. In yeast, Spp1 is a histone methyl reader that links H3K4me3 sites with the recombination machinery, promoting DSB formation. Here, we investigated whether CXXC1 has a similar function in mouse meiosis. We created two Cxxc1 conditional knockout mouse to deplete CXXC1 generally in germ cells, and before the onset of meiosis. Surprisingly, male knockout mice were fertile, and the loss of CXXC1 in spermatocytes had no effect on hotspot trimethylation, double-strand break formation or repair. Our results demonstrate that CXXC1 is not an essential link between PRDM9-activated recombination hotspot sites and DSB machinery and that the hotspot recognition pathway in mouse is independent of CXXC1.
2018-08-29 | GSE116336 | GEO
Project description:Meiotic chromosome architecture called M-bM-^@M-^\axis-loop structuresM-bM-^@M-^] and histone modifications have been demonstrated to regulate the Spo11-dependent formation of DNA double-strand breaks (DSBs) that trigger meiotic recombination. Using genome-wide chromatin immunoprecipitation (ChIP) analyses followed by deep sequencing, we compared the genome-wide distribution of the axis protein Rec8 (the kleisin subunit of meiotic cohesin) with that of oligomeric DNA covalently bound to Spo11, indicative of DSB sites. The frequency of DSB sites is overall constant between Rec8 binding sites. However, DSB cold spots are observed in regions spanning M-BM-10.8 kb around Rec8 binding sites. The axis-associated cold spots are not due to exclusion of Spo11 localization from the axis, since ChIP experiments revealed that substantial Spo11 persists at Rec8 binding sites during DSB formation. Spo11 fused with Gal4 DNA binding domain (Gal4BD-Spo11) tethered in close proximity (M-bM-^IM-$0.8 kb) to Rec8 binding sites hardly forms meiotic DSBs, in contrast with other regions. In addition, H3K4 tri-methylation (H3K4me3) remarkably decreases at Rec8 binding sites. These results suggest that reduced histone H3K4me3 in combination with inactivation of Spo11 activity on the axis discourages DSB hot spot formation. ChIP-seq analyses of Rec8, Spo11, and Gal4BD-Spo11 on budding yeast meiotic chromosomes M-bM-^@M-" Distribution of Rec8 in wt and Gal4BD-Spo11-expressing cells at 4h after meiotic induction M-bM-^@M-" Distribution of Spo11 at 3h, 4h, and 5h after meiotic induction M-bM-^@M-" Distribution of Gal4BD-Spo11 at 0h after meiotic induction
2014-03-31 | E-GEOD-52862 | biostudies-arrayexpress
Project description:DNA double-strand breaks (DSBs) are introduced in meiosis to initiate recombination and to generate crossovers, the reciprocal exchanges of genetic material between parental chromosomes. Here we present the first high-resolution map of meiotic DSBs in individual human genomes. Comparing DSB maps between individuals shows that along with DNA binding by PRDM9, additional factors dictate the efficiency of DSB formation. Furthermore, we find that in human males, the frequency of DSB formation is the primary determinant of crossover rate. Patterns of sequence polymorphisms around meiotic DSB hotspots provide evidence for both GC-biased gene conversion and for a mutagenic role of DSB repair and/or recombination. Finally, we provide compelling evidence that the aberrant repair of meiotic DSBs is a driver of human genomic disorders. Detection of meiotic double strand breaks in testis of several human male individuals.
2014-11-17 | E-GEOD-59836 | biostudies-arrayexpress
Project description:In mouse and human meiosis, DNA double strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence specific DNA binding domain of the PRDM9 histone methyl transferase. Here we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a non-canonical recruitment of PRDM9 to sites which are devoid of both, recombination activity and the PRDM9-binding consensus motif. These sites include transcription promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset of non-canonical sites also reveals DSB-independent interactions between PRDM9 and genomic sites, which include binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot bound PRDM9 and genomic sequences located on the chromosome axis.
2017-02-08 | GSE93955 | GEO