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Whole-genome nucleosome mapping in meiotic diploid S. cerevisiae

ABSTRACT: We determined nucleosome positions throughout the genome in diploid S. cerevisiae undergoing early stages of synchronous meiosis. This study sought to assess if systematic reorganization of nucleosomes occurs during meiotic prophase at or near sites of DNA double strand break formation.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE26452 | GEO | 2011/03/07

SECONDARY ACCESSION(S): PRJNA136555

REPOSITORIES: GEO

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Whole-genome nucleosome mapping in meiotic diploid S. cerevisiae

Project description:We determined nucleosome positions throughout the genome in diploid S. cerevisiae undergoing early stages of synchronous meiosis. This study sought to assess if systematic reorganization of nucleosomes occurs during meiotic prophase at or near sites of DNA double strand break formation. Six samples were sequenced, each a separate time point from either of two meiotic time courses. Dataset N1 consists of samples collected at 0, 1, 2, and 3 hr in meiosis; Dataset N2 consists of samples collected at 0 and 4 hr. Time courses, sample preparation, and sequencing were carried out in separate laboratories for the two datasets: Hochwagen lab (Whitehead Institute) for Dataset N1; Keeney lab (Howard Hughes Medical Institute; Memorial Sloan-Kettering Cancer Center) for Dataset N2.

2011-03-07 | E-GEOD-26452 | biostudies-arrayexpress

Whole-genome nucleosome mapping in meiotic diploid Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4)

Project description:We determined nucleosome positions genome-wide in diploid Saccharomyces species undergoing early stages of synchronous meiosis. This study sought to assess if meiotic DNA double-strand break formation occurred preferentially in promoter nucleosome-depleted regions in other Saccharomyces species, as it does in S. cerevisiae SK1 (Pan et al. 2011 Cell 144:719-731).

2015-08-17 | GSE71929 | GEO

Chromatin remodeler CHD8 is required for spermatogonial proliferation and early meiotic progression

Project description:Meiosis is a key step during germ cell differentiation, accompanied by the activation of thousands of genes through germline-specific chromatin reorganization. The chromatin remodeling mechanisms underpinning early meiotic stages remain poorly understood. Here we focus on the function of one of the major autism genes, CHD8, in spermatogenesis, based on the epidemiological association between autism and low fertility rates. Specific ablation of Chd8 in germ cells results in gradual depletion of undifferentiated spermatogonia as well as failure of meiotic double strand formation followed by arrest at meiotic prophase I and cell death. Transcriptional analyses demonstrate that CHD8 is required for extensive activation of spermatogenic genes in spermatogonia, necessary for spermatogonial proliferation and meiosis. CHD8 directly binds to promoters of genes crucial for meiosis, including H3K4me3 histone methyltransferase genes, meiotic cohesin genes, HORMA domain containing genes, synaptonemal complex genes, and DNA damage response genes. Through transcriptionally regulating the interaction of these meiosis-related genes, we argue that CHD8 contributes to meiotic double strand break formation and subsequent meiotic progression. Our study uncovers an essential role of CHD8 for the proliferation of undifferentiated spermatogonia and the successful progression of meiotic prophase I.

2023-12-31 | GSE252121 | GEO

ChIP-Seq experiment to analyse Zip1 localisation in the Ctf19c mutants during meiotic prophase.

Project description:The goal of this experiment is to confirm whether Ctf19c mutants affect Zip1 localisation during meiotic prophase. To do so, diploid S. cerevisiae SK1 cells were constructed containing ndt80-d to arrest cells in prophase. Cells were allowed to sporulate in sporulation media for 5 hours after which formaldehyde was added to the cultures and cells were fixed for 2hr. Samples were then processed according to the standard lab ChIP-Seq protocol (with 3 times 30cycles of 30sec of sonication) Diploid S. cerevisiae SK1 cells were constructed containing ndt80-d to arrest cells in prophase. Cells were allowed to sporulate in sporulation media for 5 hours after which formaldehyde was added to the cultures and cells were fixed for 2hr. Samples were then processed according to the standard lab ChIP-Seq protocol (with 3 times 30cycles of 30sec of sonication)

2015-12-15 | E-GEOD-70029 | biostudies-arrayexpress

The meiotic proteome in yeast - The protein expression landscape of mitosis and meiosis in diploid budding yeast

Project description:Dynamic proteome in diploid yeast cells undergoing mitotic growth and meiotic development. The proteome of growing (YPA) and differentiating yeast cells at 6 hours (SPII 6, middle meiosis) and 8 hours (SPII8, late meiosis) were compared using the TOP3 GeLC-MS/MS method.

2017-01-16 | PXD001275 | Pride

ChIP-Seq experiment to analyse Zip1 localisation in the Ctf19c mutants during meiotic prophase.

2015-12-15 | GSE70029 | GEO

Replication origin mapping of mitotic and meiotic cells in different conditions

Project description:Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase. Experiments were performed in the following strains and conditions for mitotic cells: cdc25-22 (temperature-sensitive mutation arrests cells at G2/M for synchrony, otherwise wild type), nitrogen-rich conditions; wild type, haploid and diploid, nitrogen-depletion conditions. Experiments were performed in the following strains and conditions for meiotic cells: pat1-114 diploid (temperature-sensitive mutation induces a synchronous meiosis, otherwise wild type), nitrogen-depletion and nitrogen-rich conditions; pat1-114 diploid with altered Cdc45 levels, nitrogen-depletion conditions.

2014-02-20 | GSE53879 | GEO

FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in meiotic DNA replication and recombination

Project description:The formation of RAD51/DMC1 filaments on single-stranded (ss)DNAs, which is essential for homology search and strand exchange in DNA double-strand break (DSB) repair and for the protection of stalled DNA replication forks, is tightly regulated in time and space. FIGNL1 AAA+++ ATPase plays positive and negative roles in the RAD51-mediated recombination in human cells. However, the role of FIGNL1 in gametogenesis remains unsolved. Here, we characterized a germ-line-specific conditional knockout (cKO) mouse of FIGNL1. The Fignl1 cKO male mice showed defective chromosome synapsis and impaired meiotic DSB repair with the accumulation of RAD51/DMC1 on chromosomes in mid-meiotic prophase I, supporting a role of FIGNL1 in a post-assembly stage of RAD51/DMC1 filaments. Fignl1 cKO spermatocytes accumulate RAD51 and DMC1 ensembles on chromosomes not only in early meiotic prophase I but also in meiotic S-phase. These RAD51/DMC1 assemblies are independent of meiotic DSB formation. Finally, we showed that purified FIGNL1 dismantles RAD51 filament on double-stranded (ds)DNA as well as ssDNA. These results suggest a critical role of FIGNL1 to limit the uncontrolled assembly of RAD51 and DMC1 on native dsDNAs during the meiotic S-phase and meiotic prophase I.

2023-03-31 | GSE227944 | GEO

Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference

Project description:Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference

| PRJNA1027830 | ENA

DNA intermediates of meiotic recombination in synchronous S. pombe at optimal temperature

Project description:Crossovers formed by recombination between homologous chromosomes are important for proper homolog segregation during meiosis and for generation of genetic diversity. Optimal molecular analysis of DNA intermediates of recombination requires synchronous cultures. We previously described a mutant, pat1-as2, of the fission yeast Schizosaccharomyces pombe that undergoes synchronous meiosis at 25Â°C when an ATP analog is added to the culture. Here, we compare recombination intermediates in pat1-as2 at 25Â°C with those in the widely used pat1-114 temperature-sensitive mutant at 34Â°C, a temperature higher than optimal. DNA double-strand breaks at most hotspots are similarly abundant in the two conditions but, remarkably, a few hotspots are distinctly deficient at 25Â°C. In both conditions Holliday junctions at DNA break hotspots form more frequently between sister chromatids than between homologs, but a novel species, perhaps arising from invasion by only one end of broken DNA, is more readily observed at 25Â°C. Our results confirm the validity of previous assays of recombination intermediates in S. pombe and provide new information on the mechanism of meiotic recombination. DNA double-strand break analysis by immunoprecipation of Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following meiotic induction via pat1-114 or pat1-as2 alleles

2013-09-20 | E-GEOD-49961 | biostudies-arrayexpress

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