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HSV-1 infection induces a downstream-shift of the +1 nucleosome (H2A.Z ChIPmentation)

ABSTRACT: HSV-1 infection induces a downstream-shift of the +1 nucleosome (H2A.Z ChIPmentation)

PROVIDER: PRJNA877678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21469091_1.fastq.gz	Fastqsanger.gz
	SRR21469091_2.fastq.gz	Fastqsanger.gz
	SRR21469092_1.fastq.gz	Fastqsanger.gz
	SRR21469092_2.fastq.gz	Fastqsanger.gz
	SRR21469093_1.fastq.gz	Fastqsanger.gz

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HSV-1 infection induces a downstream-shift of the +1 nucleosome (H2A.Z ChIPmentation)

Project description:HFFF cells were either mock or WT strain 17 HSV-1 infected for 8 h. Samples were processed according to the original ChIPmentation protocol (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015) with few changes as explained in the Materials and Methods section.

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The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ChIPmentation)

Project description:To look at the deposition of the histone marks in the downstream regions of DoTT genes, HFFF cells were either mock, WT HSV-1 (strain F and 17) or ΔICP22 virus infected. Throught the course of infection (for the marked samples), cells were treated with 350 ug/ml PAA. Samples were processed according to the original ChIPmentation protocol (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015) with few changes as explained in the Materials and Methods section.

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H3K4me3 ChIPmentation on HSV-1 infected primary human fibroblasts

Project description:Primary human fetal foreskin fibroblasts (HFFFs) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. ChIPmentation libraries were prepared starting with 500,000 cells per condition following the protocol described by Christian Schmidl et al, Nature Methods 2015

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H3K4me3 ChIPmentation on HSV-1 infected primary human fibroblasts

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HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes

Project description:HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes

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HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes (ATAC-seq)

Project description:We investigated transposase accessible chromatin using ATAC-seq in mock and HSV-1 strain 17 infection and infection with several HSV-1 mutants.

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The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ChIPmentation)

Project description:The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes (ChIPmentation)

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HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes (ATAC-seq)

Project description:HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes (ATAC-seq)

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Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome

Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction. Total nucleosomes from MNase-treated nuclear extracts were fractionated by sequential immunoprecipitation into homotypic H2A/H2A (AA), heterotypic H2A/H2A.Z (AZ), and homotypic H2A.Z/H2A.Z (ZZ) nucleosomes.

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The Histone Variant H2A.Z C-terminal Domain Has Locus- Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

Project description:The incorporation of histone variant H2A.Z, a conserved H2A variant, into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, including transcription. H2A.Z-containing nucleosomes may poise gene regulatory regions for transcription, but mechanistic details are lacking. In Saccharomyces cerevisiae, the diverging H2A.Z C-terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C-terminus genome wide, we made use of derivatives where the C-terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide, with the idea of regenerating the H2A.Z-dependent regulation globally. An assessment of the genome-wide distribution of these H2A.Z derivatives shows that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of the targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency vs nucleosome positioning varies enormously, depending on loci analyzed. For the ZA protein, positioning changes most importantly near origins of replication and snoRNA gene promoters, while incorporation is affected on all other sites. Furthermore, the role of H2A.Z in global transcription regulation also depends on its C-terminal region. Remarkably however, the latter mostly involves genes without a H2A.Z nucleosome in the promoter.

2022-08-18 | GSE156492 | GEO

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