Replication origin selection organizes meiotic recombination
Ontology highlight
ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
SUBMITTER: Pei-Yun Jenny Wu
PROVIDER: E-GEOD-53921 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:ChIP-on-chip analysis of Rad51 binding in cells induced to undergo synchronous meiosis after growth in continuous nitrogen-rich conditions or after nitrogen depletion. Comparison of pat1-114 cells grown in -N and +N conditions as well as pat1-114 cells with altered Cdc45 levels in -N conditions. pat1-114 rec12M-NM-^T mutants in -N and +N conditions were also evaluated to confirm that Rad51 binding is dependent on the Rec12 transesterase.
2014-02-20 | E-GEOD-53880 | biostudies-arrayexpress
Project description:ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion. Comparison of H3 and H3k4Me3 in diploid pat1-114 cells grown in -N and +N conditions.
2014-02-20 | E-GEOD-53878 | biostudies-arrayexpress
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. Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged.
2014-02-20 | E-GEOD-53879 | biostudies-arrayexpress
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:Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements, collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, which is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq datasets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as well as alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation, by functional assays including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin are generally (on chromosome 2) associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
2013-09-01 | E-MTAB-1824 | biostudies-arrayexpress
Project description:Higher-order chromosome structure is assumed to control various DNA-templated reactions in eukaryotes. Meiotic chromosomes implement developed structures called M-bM-^@M-^\axesM-bM-^@M-^] and M-bM-^@M-^\loopsM-bM-^@M-^]; both are suggested to tether each other, activating Spo11 to catalyze meiotic DNA double-strand breaks (DSBs) at recombination hotspots. We found that the Schizosaccharomyces pombe Spo11 homolog Rec12 and its partners form two distinct subcomplexes, DSBC (Rec6-Rec12-Rec14) and SFT (Rec7-Rec15-Rec24). Additionally, Mde2, whose expression is strictly regulated by the replication checkpoint, interacts with a component of each subcomplex. The SFT subcomplex binds to both axes via direct interaction of Rec15 with Rec10 in axes and DSB sites, hence axial Rec10 can partially tether DSB sites located in loops. Importantly, this multiprotein-based tethered axis-loop complex is destabilized in the absence of Mde2. We therefore propose a novel mechanism by which Mde2 functions as a recombination initiation mediator to tether axes and loops, in liaison with the meiotic replication checkpoint. ChIP-chip analyses of Rec10 (in wild type), Mde2 (in wild type and rec15M-bM-^HM-^F), and Rec15 (in wild type, rec10M-bM-^HM-^F, rec24M-bM-^HM-^F and mde2M-bM-^HM-^F) at meiosis 4 hours.
2012-07-27 | E-GEOD-31846 | 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.
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Project description:To identify genes that are activated during meiosis and tell the effect of mei4 on different genes at 0 and 5 hours after meiotic induction.
2008-09-26 | E-TABM-465 | biostudies-arrayexpress
Project description:Occupancy profiling of Rec12 during fission yeast meiosis. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered by Rec12 ChIP from fission yeast undergoing synchronous meiosis were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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