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Series GSE74355 Query DataSets for GSE74355
Status Public on May 04, 2016
Title The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Comprehensive analysis of global ATF3-binding profiles in the human genome under quiescent and stressed (DNA damage) conditions. Although expressed at a low level, quiescent ATF3 was found to bind a large number of genomic sites that are often associated with genes required for cellular stress responses. While these ATF3-binding sites often contained motifs for other transcription factors (TFs), we found that ATF3 bound a large portion of active enhancers characterized by p300 binding, and as a consequence, ATF3 often regulates expression of the genes proximal to these enhancers. While DNA damage elicited by camptothecin dramatically altered the ATF3 binding profile, most of the genes regulated by ATF3 upon DNA damage were pre-bound by ATF3 before the stress. Moreover, we demonstrated that ATF3 was co-localized with the major stress responder p53 at genomic sites, thereby contributing to induction of p53 target gene expression upon DNA damage. Therefore, our results suggest that ATF3 bookmarks genomic sites and interacts with other TFs for transcriptional regulation under quiescent and stressed conditions.
 
Overall design ATF3-knockout HCT116 cells were generated by AAV-mediated homologous recombination. ATF3-wildtype (ATF3-WT), -knockout (ATF3-KO), p53-knockout (p53-KO) cells were treated with DMSO (Ctrl) or 1.5 uM of camptothecin (CPT) for 4 h, and then crosslinked by 1 mM of di(N-succinimidyl) glutarate (DSG) for 45 min and 1% of formaldehyde for 10 min. Chromatin was immunoprecipitated with 2 ug of ATF3 antibody (Santa Cruz, cat.# sc-188, lot# F2614) or p53 antibody (Santa Cruz, cat.# sc-126, lot# L3013) and subjected to ChIP-seq analyses.
 
Contributor(s) Yan C, Zhao J
Citation(s) 27146783
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Jindan Yu
E-mail(s) jindan-yu@northwestern.edu
Organization name Northwestern University
Department Division of Hematology/Oncology
Lab Jindan Yu's lab
Street address 303 E. Superior St., Lurie 5-117
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platforms (1)
GPL15456 Illumina HiScanSQ (Homo sapiens)
Samples (5)
GSM1917770 ATF3-CPT
GSM1917771 ATF3-KO
GSM1917772 p53-CPT
This SubSeries is part of SuperSeries:
GSE74363 The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation
Relations
BioProject PRJNA299821
SRA SRP065278

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Supplementary file Size Download File type/resource
GSE74355_RAW.tar 204.8 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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