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| Status |
Public on Sep 27, 2016 |
| Title |
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1−/−) or depletion (Nrf2−/−) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response.
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| Overall design |
We performed a ChIP-Seq experiment with Keap1−/− MEFs, in which Nrf2 is protected from ubiquitination and degradation, constitutively activating the expression of Nrf2 target genes. We generated two DNA libraries using two Nrf2-specific antibodies (one monoclonal and one polyclonal). A third control library contains the input DNA.
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| Contributor(s) |
Biswal S, Wasserman WW, Portales-Casamar E, Arenillas DJ |
| Citation(s) |
20460467 |
| Submission date |
Sep 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shyam Biswal |
| Organization name |
Johns Hopkins Bloomberg School of Public Health
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| Department |
Environmental Health Sciences
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| Lab |
Biswal
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| Street address |
615 N. Wolfe St.
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA344482 |
| SRA |
SRP090470 |
