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Genome-wide analysis of ATF4 binding in histidinol-treated cells and RNA-Seq experiment to identify genes regulated by ATF4

ABSTRACT: Genome-wide analysis of ATF4 binding in histidinol-treated cells and RNA-Seq experiment to identify genes regulated by ATF4

PROVIDER: PRJNA285115 | ENA |

REPOSITORIES: ENA

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RNA-Seq experiment to identify genes regulated by ATF4

2015-08-28 | GSE69308 | GEO

RNA-Seq experiment to identify genes regulated by ATF4

Project description:Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide profiling of ATF4-dependent RNA expression in human HAP-1 cells. HAP-1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We analyzed WT and ATF4 KO cells. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol. RNA expression profiles were generated for WT and ATF4 KO HAP1 cells. ATF4 genes were mutated using Cas9 genome editing technology. Amino acid starvation was mimicked by treating WT and ATF4 KO cells with 2 mM histidinol for 24 hours, which increases ATF4 expression.

2015-08-28 | E-GEOD-69308 | biostudies-arrayexpress

Genome-wide analysis of ATF4 binding in histidinol-treated cells

2015-08-28 | GSE69304 | GEO

Genome-wide analysis of ATF4 binding in histidinol-treated cells

Project description:Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide occupancy profiling of ATF4 in human HAP1 cells. HAP1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol. We identified peaks of ATF4 binding using three independent antibodies. Examination of ATF4 binding in HAP1 cells treated with 2 mM histidinol for 24 hours.

2015-08-28 | E-GEOD-69304 | biostudies-arrayexpress

ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP

Project description:We report the direct target genes of ATF4 and CHOP in response to endoplasim reticulum stress through next generation sequencing. By obtaining genowide sequence from chromatin immunoprecipitated DNA with anti-CHOP and anit-ATF4, we identified direct binding sites of ATF4 and CHOP in promoter regions of their target genes in mouse embrynic fibroblasts (MEFs) in response to ER stress. In addition, we obtained list of genes which are differentially regulated in Atf4 or Chop-deficient MEFs compared to the wild-type MEFs in response to ER stress. We found that genes related with unfolded protein response and protein synthesis were directly regulated by ATF4 and CHOP. Through this observation, we conclude that main role of ATF4 and CHOP as transcription factors is to enhance mRNA translation in respone to ER stress. This sutdy provide new insight of genetic network of ATF4 and CHOP in response to ER stress. For ChIP-seq, Chop+/+ and Chop-/- MEFs were treated with Tunicamycin, N-glycosylation inhibitor, to induce ER stress for 8hr. Atf4+/+ and Atf4-/- MEFs were also treated same condition for ChIP-Seq. For mRNA-seq, wild-type, Atf4-/-, and Chop-/- MEFs were treated with tunicamycin for 8hr for experiments.

2013-04-11 | E-GEOD-35681 | biostudies-arrayexpress

Genome-wide analysis of ATF4 binding in histidinol-treated cells and RNA-Seq experiment to identify genes regulated by ATF4

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

2015-08-28 | GSE69309 | GEO

ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP

2013-04-11 | GSE35681 | GEO

Homo sapiens

Project description:RNA-Seq experiment to identify genes regulated by ATF4

| PRJNA285117 | ENA

Genome-wide analysis of ATF4 binding in histidinol-treated cells and RNA-Seq experiment to identify genes regulated by ATF4

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-28 | E-GEOD-69309 | biostudies-arrayexpress

Global proteome analysis of ATF4 targets during ER stress.

Project description:Cancer cells exploit many of the cellular adaptive responses to support their survival needs. One such critical pathway in eukaryotic cells is the unfolded protein response (UPR) that is important in normal physiology as well as disease states, including cancer. Since UPR can serve as a lever between survival and death, regulated control of its activity is critical for tumor formation and growth although the underlying mechanisms are poorly understood. Here we show that one of the main transcriptional effectors of UPR, activating transcription factor 4 (ATF4), is essential for prostate cancer (PCa) growth and survival. To identify ATF4 target genes that mediate the ISR outcome and to get insight into its mechanism of action in PCa, we performed global proteomic expression profiling in parallel with transcriptomic expression profiling. These data show that ATF4 regulates important metabolic pathways in PCa cells.

2019-07-22 | PXD012858 | Pride

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