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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

ABSTRACT: Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

PROVIDER: PRJNA943526 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23823700_1.fastq.gz	Fastqsanger.gz
	SRR23823700_2.fastq.gz	Fastqsanger.gz
	SRR23823701_1.fastq.gz	Fastqsanger.gz
	SRR23823701_2.fastq.gz	Fastqsanger.gz
	SRR23823702_1.fastq.gz	Fastqsanger.gz

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq]

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [Mnase-seq]

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Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

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

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H2B mono-ubiquitylation facilitates fork stalling and recovery during replication stress by coordinating Rad53 activation and chromatin assembly

Project description:The influence of mono-ubiquitylation of histone H2B (H2Bub) on transcription via nucleosome reassembly has been widely documented. Recently, it has also been shown that H2Bub promotes recovery from replication stress; however, the underling molecular mechanism remains unclear. Here, we show that H2B ubiquitylation coordinates activation of the intra-S replication checkpoint and chromatin re-assembly, in order to limit fork progression and DNA damage in the presence of replication stress. In particular, we show that the absence of H2Bub affects replication dynamics (enhanced fork progression and reduced origin firing), leading to γH2A accumulation and increased hydroxyurea sensitivity. Further genetic analysis indicates a role for H2Bub in transducing Rad53 phosphorylation. Concomitantly, we found that a change in replication dynamics is not due to a change in dNTP level, but is mediated by reduced Rad53 activation and destabilization of the RecQ helicase Sgs1 at the fork. Furthermore, we demonstrate that H2Bub facilitates the dissociation of the histone chaperone Asf1 from Rad53, and nucleosome reassembly behind the fork is compromised in cells lacking H2Bub. Taken together, these results indicate that the regulation of H2B ubiquitylation is a key event in the maintenance of genome stability, through coordination of intra-S checkpoint activation, chromatin assembly and replication fork progression. S.cerevisiae oligonucleotide microarrays were provided by Affymetrix (S.cerevisiae Tiling 1.0R, P/N 900645). BrdU and proteins ChIP-chip analyses were carried out as described (Fachinetti et al., M Cell, 2010).

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Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex [RNA-Seq]

Project description:we use an induced degron system to study how rapid clearance of ATP-dependent chromatin remodelers affect nucleosome locations. 1. Screening eight remodelers 2. depletion of Sth1 leads to rapid and reversible fill-in of nucleosome-free regions at gene promoters. 3. changes at depletion and recovery do not depend on major chromatin reassembly during DNA replication. 4. RSC is crucial in maintaining open promoters of low expressed genes. RSC is not directly required for an acute transcriptional response. 5. Changes in nucleosome positions are tightly related to the specific TSS usage at promoters.

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Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodeling Complex [MNase-Seq]

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Topoisomerase II binds nucleosome-free DNA and acts redundantly with Topoisomerase I to enhance recruitment of RNA Pol II in budding yeast

Project description:DNA topoisomerases are known to promote transcription in prokaryotes by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome free. However, while nucleosome loss enables Top2 occupancy the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enable Top2 binding which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.

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