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Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq]

ABSTRACT: Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq]

PROVIDER: PRJNA1111581 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29025600_1.fastq.gz	Fastqsanger.gz
	SRR29025600_2.fastq.gz	Fastqsanger.gz
	SRR29025601_1.fastq.gz	Fastqsanger.gz
	SRR29025601_2.fastq.gz	Fastqsanger.gz
	SRR29025602_1.fastq.gz	Fastqsanger.gz

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Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq]

Project description:Transcription-replication conflicts (TRCs) can provoke genome instability. Progressing transcription and replication machineries profoundly impact their underlying chromatin template and thus, conflict sites are vulnerable to chromatin and epigenome alterations. Here, we engineered an inducible TRC reporter system using a genome-integrated R-loop-prone sequence. Using this system, we characterized the dynamic changes of the local chromatin structure inflicted by TRCs, leading to reduced nucleosome occupancy and replication fork blockage. Consequently, inducing a handful TRCs on the genome results in a measurable global replication stress response. We also find a TRC-specific increase in H3K79 methylation at the R-loop forming TRC-site. Accordingly, inhibition of the H3K79 methyltransferase DOT1L leads to increased cellular TRCs and exacerbated DNA damage response, suggesting that deposition of this mark is required for effective detection and resolution of TRCs. Thus, our work highlights the molecular dynamics and reveals specific epigenetic modifiers bookmarking TRC sites, relevant to cancer and other diseases.

2025-05-01 | GSE267495 | GEO

Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction

Project description:Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction

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Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [WGS]

Project description:Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [WGS]

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Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [BrdUseq]

Project description:Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [BrdUseq]

| PRJNA1111582 | ENA

Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [WGS]

2025-05-01 | GSE268016 | GEO

Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [BrdUseq]

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Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

Project description:Chaperones, nucleosome remodeling complexes and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these co-factors function ubiquitously, and the impact of nucleosome eviction on transcription genome-wide, are poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple co-factors to address these issues for ~200 genes belonging to the Gcn4 transcriptome, of which ~70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation. Examining four target genes in a panel of mutants indicated that SWI/SNF, Gcn5, the Hsp70 co-chaperone Ydj1, and chromatin-associated factor Yta7 are required downstream of Gcn4 binding for robust H3 eviction in otherwise wild-type cells. Using ChIP-seq to interrogate all 70 exemplar genes in single, double and triple mutants implicated Gcn5, Snf2 and Ydj1 in H3 eviction at most, but not all Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these 3 co-factors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in co-factor mutants was coupled with reduced Pol II occupancies for the Gcn4 transcriptome and the most highly expressed uninduced genes, but the relative Pol II levels at most genes were unaffected or even elevated. These findings indicate that nucleosome eviction is crucial for robust transcription of highly expressed genes, but that other steps in gene activation are more rate-limiting for most other yeast genes. Chromatin immunoprecipitated DNA from WT (induced(+SM) and uninduced(no SM)) and mutants (induced(+SM)) followed by paired-end sequencing. Nucleosomal DNA obtained by MNase digestion were also subjected to paired-end sequencing.

2015-11-09 | E-GEOD-74787 | biostudies-arrayexpress

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation

Project description:The experiment was performed to assess the importance of nucleosome eviction for the binding of condensin to chromatin during mitosis. The condensin complex associates with chromatin during mitosis to ensure chromosome condensation and accurate segregation, but how this binding is achieved remains poorly understood. Our study indicates that transcription co-activators Gcn5 and Mst2 assist condensin binding during mitosis by evicting nucleosomes. To reach this conclusion, we mapped nucleosomes, during mitosis, in wild-type and gcn5mst2 mutant strains. This experiment allowed us (1) to identify nucleosome-depleted regions (ndrs) during mitosis and to show that condensin tends to colocalize with ndr at the 3ends of genes, and (2) to confirm the importance of nucleosome eviction from ndrs by gcn5 and mst2, during mitosis, for the binding of condensin to chromatin.this experiment determines the patterns of nucleosomes in wild type and mutant fission yeast cells arrested in early mitosis. We analysed wild-type cells, cells lacking Gcn5 histone acetylatransferase (gcn5D) and cells lacking both Gcn5 and Mst2 histone acetyltransferases (Gcn5Dmst2D). All cells used in this study expressed a GFP-tagged version of condensin (Cnd2-GFP) and were blocked in early mitosis at 19C by the nda3-KM311 mutation. Mitotic indexes were determined by scoring the accumulation of Cnd2-GFP in the nucleus. Mitotic cells were collected and chromatin was digested by increasing amount of MNase to produce mononucleosomes. Mononucleosomal DNA was purified on an agarose gel and sequence on an Illumina Nextseq 500 apparatus. Three replicates of wild type, gcn5D and gcn5Dmst2D were analysed. Nucleosome patterns were determined in wild-type cells, cells lacking Gcn5 and cells lacking both Gcn5 and Mst2.

2016-04-18 | E-MTAB-4620 | biostudies-arrayexpress

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation

Project description:Nucleosome eviction in mitosis assists condensin loading and chromosome condensation

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Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

2015-11-09 | GSE74787 | GEO