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| 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
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| 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.
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| 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.
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| Contributor(s) |
Yan C, Zhao J |
| Citation(s) |
27146783 |
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| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
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| Organization name |
Emory University
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| Department |
Urology
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| Lab |
Jindan Yu's lab
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| Street address |
E330, 1760 Haygood Dr NE
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platforms (1) |
| GPL15456 |
Illumina HiScanSQ (Homo sapiens) |
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| Samples (5)
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| This SubSeries is part of SuperSeries: |
| GSE74363 |
The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation |
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| Relations |
| BioProject |
PRJNA299821 |
| SRA |
SRP065278 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74355_RAW.tar |
204.8 Mb |
(http)(custom) |
TAR (of BEDGRAPH, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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