RNA-seq analysis in syp-2::AID and N2 controls with and without auxin treatment (4 hours at 4 mM concentration)
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE134989 | GEO | 2020/06/17
REPOSITORIES: GEO
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Project description:Meiotic DSB, catalyzed by the Spo11 transesterase protein and accessory DSB proteins, form in the nucleosome depleted regions (NDR) at promoters, preferentially those located on the chromosome loops that shape meiotic chromosomes, whereas the DSB proteins are located on chromosome axes at the basis of these loops. Mechanisms bridging these two chromosomal regions for DSB formation have remained elusive. Here we show that Spp1, a conserved member of the histone H3K4 methyltransferase Set1 complex, is required for normal levels of DSB formation and is associated with chromosome axes in the DSB-rich domains during meiosis. Moreover, Spp1 physically interacts with the Mer2 axis-associated DSB protein, and uses its PHD finger as a magnet to read H3K4 trimethylation close to promoters, tether these regions to chromosome axes and activate cleavage in the nearby promoter by the DSB proteins. We further show that in the absence of Spp1 or the Set1 complex, DSB are introduced at a few new sites, located in promoters of transcriptionally induced genes, suggesting another selection mechanism of preferred DSB sequences. This paper provides the molecular mechanism linking H3K4me3 to the DSB forming machinery, by the meiosis-specific specialization of Spp1 as an active member of the DSB complex and a reader of H3K4me3, and opens perspectives for the study of DSB formation at mammalian recombination hotspots that are also enriched in H3K4me3. ChIP-chip experiment in vegetative or meiotic diploid SK1 yeast cells - two biological replicates
2012-12-13 | E-GEOD-39900 | biostudies-arrayexpress
Project description:Meiotic DSB, catalyzed by the Spo11 transesterase protein and accessory DSB proteins, form in the nucleosome depleted regions (NDR) at promoters, preferentially those located on the chromosome loops that shape meiotic chromosomes, whereas the DSB proteins are located on chromosome axes at the basis of these loops. Mechanisms bridging these two chromosomal regions for DSB formation have remained elusive. Here we show that Spp1, a conserved member of the histone H3K4 methyltransferase Set1 complex, is required for normal levels of DSB formation and is associated with chromosome axes in the DSB-rich domains during meiosis. Moreover, Spp1 physically interacts with the Mer2 axis-associated DSB protein, and uses its PHD finger as a magnet to read H3K4 trimethylation close to promoters, tether these regions to chromosome axes and activate cleavage in the nearby promoter by the DSB proteins. We further show that in the absence of Spp1 or the Set1 complex, DSB are introduced at a few new sites, located in promoters of transcriptionally induced genes, suggesting another selection mechanism of preferred DSB sequences. This paper provides the molecular mechanism linking H3K4me3 to the DSB forming machinery, by the meiosis-specific specialization of Spp1 as an active member of the DSB complex and a reader of H3K4me3, and opens perspectives for the study of DSB formation at mammalian recombination hotspots that are also enriched in H3K4me3.
2012-12-13 | GSE39900 | GEO
Project description:The H2A.Z histone variant is deposited into chromatin by the SWR1 complex affecting multiple aspects of meiosis. Here we describe a SWR1-independent localization of H2A.Z at meiotic telomeres and the centrosome. We demonstrate that H2A.Z colocalizes and interacts with Mps3, the SUN component of the LINC complex that spans the nuclear envelope and links meiotic telomeres to the cytoskeleton promoting meiotic chromosome movement. H2A.Z also interacts with the meiosis-specific Ndj1 protein that anchors telomeres to the nuclear periphery via Mps3. Telomeric localization of H2A.Z depends on Ndj1 and the N-terminal domain of Mps3. Although telomeric attachment to the nuclear envelope is maintained in the absence of H2A.Z, the distribution of Mps3 is altered. The velocity of chromosome movement during meiotic prophase I is reduced in the htz1? mutant lacking H2A.Z, but it is unaffected in swr1? cells. We reveal that H2A.Z is an additional LINC-associated factor that contributes to promote telomere-driven chromosome motion critical for error-free gametogenesis.
2020-11-16 | GSE153003 | GEO
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:Spo11-mediated DNA double strand breaks (DSBs) that initiate meiotic recombination are temporally and spatially controlled. The meiotic cohesin Rec8 has been implicated in regulating DSB formation, but little is known about the features of their interplay. To shed light on this point, we investigated the genome-wide localization of Spo11 in budding yeast during early meiosis by chromatin immunoprecipitation using high-density tiling arrays. We found that Spo11 is dynamically localized to meiotic chromosomes. Spo11 initially accumulated around centromeres and thereafter localized to arm regions as premeiotic S-phase proceeded. During this stage, a substantial proportion of Spo11 bound to Rec8 binding sites. Eventually, some of Spo11 further bound to both DSB and Rec8 sites. We also showed that such a change in a distribution of Spo11 is affected by hydroxyurea (HU) treatment. Interestingly, deletion of REC8 influences the localization of Spo11 to centromeres and in some of the intervals of the chromosomal arms. Thereby we observed a lack of DSB formation in a region-specific manner. These observations suggest that Rec8 would prearrange the distribution of Spo11 along chromosomes and will provide clues to understanding temporal and spatial regulation of DSB formation. Keywords: ChIP-chip â?¢ The goal of the experiment Genome-wide localization of Spo11, Mre11, Rec8, and DSB sites on meiotic chromosomes in Saccharomyces cerevisiae â?¢ Keywords Meiosis, Meiotic homologous recombination, Premeiotic DNA replication, cohesin, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI), Spo11, Mre11, Rec8, DSB (Double strand break) â?¢ Experimental factor Distribution of Spo11, Mre11, and Rec8 in wild type in early meiosis (1.5 hrs, 2 hrs, 3 hrs, 4 hrs, and 5 hrs in sporulation medium) Distribution of Spo11 in rec8delta cells in early meiosis (1.5 hrs, 2 hrs, 3 hrs, 4 hrs, and 5 hrs in sporulation medium) Distribution of Spo11 in wild type in the presence of HU (2hrs and 4 hrs in sporulation medium containing HU) Distribution of DSB sites in rad50S mutant cells at 7 hrs in sporulation medium Distribution of DSB sites in rec8delta rad50S mutant cells at 7 hrs in sporulation medium â?¢ Experimental design ChIP analyses: SK1 background cells expressing FLAG tagged protein were used for the ChIP using anti-FLAG M2 antibody. ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI and rikDACF for chromosome VI) were used. Mapping of DSB sites: DSB rich fraction was concentrated by ChIP of Spo11-FLAG in rad50S mutant without crosslinking. In the mutant, DSBs ramain unrepaired with covalently attached Spo11.Meiotic cells (at 7 hours in sporulation medium) were used for the analyses. â?¢ Quality control steps taken Confirmation of several loci by quantitative real time PCR. Southern blotting of several DSB sites.
2010-05-18 | E-GEOD-8422 | biostudies-arrayexpress
Project description:Meiotic recombination is initiated by the Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions known as hotspots, but the factor(s) which specify the positions for meiotic DSB hotspots remain unclear. Here, we show that the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, change dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage, and found they co-localize with meiotic DSB hotspots. We further show that transcription-replication head-on collisions could promote R-loop formation during meiosis, and apparently direct the initiation of meiotic DSB formation. Furthermore, the hotspots can be eliminated by reverse the direction of either transcription or replication, and reconstituted by reverse both of their direction. Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.
2023-05-14 | GSE167915 | GEO
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:To determine meiotic recombination initiation sites in Arabidopsis thaliana genome we purified and sequenced oligonucleotides (35-45 nt) bound to SPO11-1, meiosis specific transesterase that induces meiotic DSB formation. This reveals that SPO11-1-oligonucleotide hotspots occur at nucleosome depleted regions of gene promoters, introns, terminators and specific families of DNA transposons (recomposons). To investigate the influence of chromatin structure and epigenetic factors on meiotic DSB formation we performed sequencing of SPO11-1-oligonucleotides in arp6, met1 and suvh4 suvh5 suvh6.
2017-06-05 | E-MTAB-5041 | biostudies-arrayexpress
Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.
2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress
Project description:Meiosis occurs in all sexually reproducing unicellular and multicellular eukaryotes. Bouquet formation is indispensible for homologous pairing or recombination during meiotic prophase I, but the regulatory mechanism of this process remain largely unknown. Cyclins regulate the precise meiosis progression by activating cyclin-dependent kinases. We therefore investigated the functional contribution of cyclin Cyc2p during bouquet (named crescent in Tetrahymena) formation in Tetrahymena thermophila. As a conjugation specific gene, CYC2 expression is significantly upregulated at 2-4 h after the initiation of conjugation and Cyc2p mainly localized in cytoplasm as well as weakly in the meiotic micronucleus (Mic). CYC2 knockout mutants failed to form elongated crescent structure and aborted meiotic development. Mic DNA double-strand breakage (DSB) decreased in ΔCYC2 cells as shown by γ-H2A.X staining, consistent with the finding that expression level of SPO11, DMC1, and RAD51 decreased in ΔCYC2 cells. However, ΔCYC2 cells failed to form crescent structure when artificial DSBs were induced, indicating that the inability to enter crescent phase was not completely due to the lack of DSBs. The localization of tubulin showed that impaired structure of nuclei and nuclear membrane may contribute to the blocked Mic elongation. This is further supported by the observation that expression levels of two microtubule associated kinesin genes, KIN11 and KIN141, were significantly downregulated in ΔCYC2 cells. Interestingly, scnRNA accumulation seemed intact in ΔCYC2 cells whereas the intensity of the heterochromatin marker H3K23me3 was abnormally increased. Together, these results showed that cyclin Cyc2p is required for micronuclear meiosis by controlling meiotic prophase chromosome breakage and the microtubule movement of nuclei in Tetrahymena.
2018-12-14 | GSE108064 | GEO