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H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

ABSTRACT: H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

PROVIDER: PRJNA543885 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9097590.fastq.gz	Fastqsanger.gz
	SRR9097591.fastq.gz	Fastqsanger.gz
	SRR9097592.fastq.gz	Fastqsanger.gz
	SRR9097587.fastq.gz	Fastqsanger.gz
	SRR9097588.fastq.gz	Fastqsanger.gz

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H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

Project description:T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

2019-05-21 | GSE131511 | GEO

ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses [ChIP-seq]

Project description:CD8+ T cells are critical for the adaptive immune response to infection and tumors. Moreover, CD8+ T cell memory is important for the immune systems response to repeat infections. Here, we identify the activating transcription factor 7 interacting protein as a critical regulator of CD8+ T cell memory and effector responses. Mice with a T cell specific deletion of ATF7ip have a CD8+ T cell intrinsic enhancement of Il7r expression and Il2 expression leading to enhanced memory responses. ChIP-seq studies identified ATF7ip as an inhibitor of Il7r and Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il7r gene loci and Il2-Il21 intergenic region. Interestingly, ATF7ip targeted transposable elements (TE) for H3K9me3 in these regions. These results demonstrate a new epigenetic pathway by which IL7r and IL-2 production are constrained in CD8+ T cells, and this may open up new avenues for modulating their production.

2021-12-21 | GSE190624 | GEO

RNA-seq of ATF7ip-deficient T cells

Project description:RNA-seq performed in ATF7ip-deficient T cells reveals a defect in Th17 gene induction secondary to increased IL-2 T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

2019-05-21 | GSE131533 | GEO

ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses

Project description:Method: To study the effector response of Atf7ip, a) we infected Atf7ip+/fl and Atf7ipfl/fl mice with lcmv . RNAseq was performed using CD8 T cells isolated from Lymph node and Spleen of Het and KO mice. RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. The RNA-Seq was performed by UCSF core using Illumina Platform. RNAseq was also carried out using naive CD8 T cells isolated from Atf7ip+/fl and Atf7ipfl/fl mice along with Atf7ip+/fl and Atf7ipfl/fl CD8 T cells stimulated for 72 hrs. This set of samples were sequenced using commercial facility from Genewiz, USA. Results: Our transcriptome analysis (RNA-seq) identified, Il7r, Runx3 etc. to be upregulated in the Atf7ipfl/fl CD8 T cells as compared to the Atf7ip+/fl CD8 T cells.

2021-12-21 | GSE190417 | GEO

Assessing the impact of loss of ATF7IP and SETDB1 on the global distribution of H3K9me3

Project description:By comparing HeLa cells lacking ATF7IP or SETDB1 generated through CRISPR/Cas9-mediated gene disruption to wild-type HeLa cells, the goal of the experiment was to determine the effect of loss of the SETDB1•ATF7IP complex on the distribution of the repress

2016-10-11 | GSE86811 | GEO

ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses [ChIP-seq]

Project description:ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses [ChIP-seq]

| PRJNA787789 | ENA

H3K9me3 and H3K9Ac ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

Project description:H3K9me3 and H3K9Ac ChIP-Seq performed on naïve WT and TRIM28KO CD4 T cells

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Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations [ChIP-seq]

Project description:We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits the interaction of the ATF7IP-SETDB1 complex with other heterochromatin regulators and transcriptional repressors, maintaining low levels of H3K9 trimethylation (H3K9me3) in hESCs. Conversely, loss of HTT promotes global increased H3K9me3 levels. To test whether HTT knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3.

2018-09-04 | GSE118324 | GEO

ChIP-chip of H3K9me3 in Drosophila at different time points of development

Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This Series contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM382158..GSM382166]: ChIP-chip of H3K9me3 in Drosophila embryos at 12-16 hours of development [GSM384690..GSM384698]: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development [GSM384723..GSM384731]: ChIP-chip of H3K9me3 in Drosophila embryos at 4-8 hours of development [GSM384732..GSM384740]: ChIP-chip of H3K9me3 in Drosophila embryos at 16-20 hours of development [GSM384741..GSM384749]: ChIP-chip of H3K9me3 in Drosophila embryos at 20-24 hours of development [GSM384750..GSM384758]: ChIP-chip of H3K9me3 in Drosophila L1 larvae [GSM384760..GSM384768]: ChIP-chip of H3K9me3 in Drosophila L2 larvae [GSM418207..GSM418215]: ChIP-chip of H3K9me3 in Drosophila Adult male [GSM418216..GSM418224]: ChIP-chip of H3K9me3 in Drosophila embryos at 8-12 hours of development [GSM442371..GSM442379]: ChIP-chip of H3K9me3 in Drosophila Adult male - Set2 [GSM442380..GSM442388]: ChIP-chip of H3K9me3 in Drosophila Pupae [GSM442389..GSM442397]: ChIP-chip of H3K9me3 in Drosophila L3 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.

2010-06-22 | E-GEOD-15422 | biostudies-arrayexpress

ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses

Project description:ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses

| PRJNA787083 | ENA