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

ABSTRACT: 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)

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE70029 | GEO | 2015/12/15

SECONDARY ACCESSION(S): PRJNA287518

REPOSITORIES: GEO

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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

Rec8 ChIP-Seq experiment to analyse cohesin localisation in the Ctf19c mutants during meiotic prophase.

Project description:Ctf19c mutants were shown to specifically impair cohesin localisation at the pericentromere during mitosis. The goal of this experiment is to confirm whether this mutant has the same effect on cohesin localisation during meiotic prophase. To do so, diploid S. cerevisiae SK1 cells were constructed containing Rec8-3HA in an ndt80-d background. 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 Rec8-3HA in an ndt80-d background. 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-70030 | biostudies-arrayexpress

Rec8 ChIP-Seq experiment to analyse cohesin localisation in the Ctf19c mutants during meiotic prophase.

2015-12-15 | GSE70030 | GEO

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

Project description:During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early—revealing regions of preferential priming—but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering—a phenomenon that is exacerbated in tel1∆ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.

2023-10-18 | GSE245327 | GEO

ChIP-Seq experiments to analyse Rec8 and Zip1 localisation in Ctf19c mutants during meiotic prophase

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

2015-12-15 | GSE70032 | GEO

ChIP-Seq experiments to analyse Rec8 and Zip1 localisation in Ctf19c mutants during meiotic prophase

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-15 | E-GEOD-70032 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae mre11, rad50 and spo11 mutants in premeiosis and meiotic prophase

Project description:Mre11, together with Rad50 and Xrs2/NBS, plays pivotal roles in homologous recombination, repair of DNA double strand breaks (DSBs), activation of damage-induced checkpoint, and telomere maintenance. Using DNA microarray assays to analyze yeast mutants (mre11delta, rad50delta, and spo11Y135F) defective for meiotic DSB formation, we demonstrate that the absence of Mre11 in yeast causes specific effects on regulation of a class of meiotic genes for spore development. The transcriptional deficiency was not observed in other DSB mutants such as rad50delta and spo11Y135F, suggesting the transcriptional defect in mre11delta is due to neither lack of meiotic DSB formation, nor disintegrity of Mre11-Rad50-Xrs2 complex.These defects were confirmed by northern and lacZ reporter gene assays. Experiment Overall Design: Gene expression data from wild type, mre11delta, rad50delta, and spo11Y135F cells in premeiosis (meiosis 0 hr) and prophase (meiosis 4 hr). Affymetrix GeneChip YG-S98 was used. All strains used were SK1 background diploid cells.

2007-10-23 | E-GEOD-6620 | biostudies-arrayexpress

MEIOC interacting proteins during meiotic prophase I

Project description:The meiosis-specific chromosomal events of homolog pairing, synapsis, and recombination occur over an extended meiotic prophase I. In this study, we show that, in mice, maintenance of an extended meiotic prophase I requires the gene Meioc, a germ-cell specific factor conserved in most metazoans. Using immunoprecipitation and quantitative mass spectrometry, we identify proteins that interact with MEIOC in the mouse germ line.

2017-03-27 | PXD005473 | Pride

Dynamic Reorganization of the Genome Shapes the Recombination Landscape in Meiotic Prophase

Project description:In meiotic prophase, chromosomes are organized into compacted loop arrays to promote homolog pairing and recombination. Here, we probe the architecture of the mouse spermatocyte genome in early and late meiotic prophase using Hi-C. We show that early-prophase chromosomes are arranged as linear arrays of 0.8-1 Mb loops, which extend to 1.5-2 Mb in late prophase as chromosomes compact and homologs undergo synapsis. Topologically associating domains (TADs) are lost in meiotic prophase, suggesting that assembly of the meiotic chromosome axis dramatically reduces the dynamics of chromosome-associated cohesin complexes. While TADs are lost, physically-separated A and B compartments are maintained in meiotic prophase. Moreover, meiotic DNA breaks and inter-homolog crossovers preferentially form in the gene-dense A compartment, revealing a role for chromatin organization in meiotic recombination. Finally, direct detection of inter-homolog contacts genome-wide reveals the structural basis for homolog alignment and juxtaposition by the synaptonemal complex.

2018-11-17 | GSE122622 | GEO

Transcriptome analysis of meiotic prophase spermatocytes in Zfp541 +/- and Zfp541 KO mice

Project description:ZFP541 is one of the candidates for a transcriptional regulator during mouse meiotic prophase. In order to address the role of ZFP541, transcriptomes of meiotic prophase-enriched population were compared between Zfp541 +/- and Zfp541 KO testes by RNA-seq. The meiotic prophase-enriched population was isolated from Zfp541 +/- and Zfp541 KO testes at postnatal day 18 (P18), on the Rec8-3FH-GFP KI background by fluorescent sorting of GFP positive cells.

2020-12-29 | GSE163917 | GEO

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