Identification of novel NRF2-regulated genes by ChIP-Seq: influence on retinoid X receptor alpha.

Nucleic Acids Research
Brian N ChorleyDouglas A Bell

Abstract

Cellular oxidative and electrophilic stress triggers a protective response in mammals regulated by NRF2 (nuclear factor (erythroid-derived) 2-like; NFE2L2) binding to deoxyribonucleic acid-regulatory sequences near stress-responsive genes. Studies using Nrf2-deficient mice suggest that hundreds of genes may be regulated by NRF2. To identify human NRF2-regulated genes, we conducted chromatin immunoprecipitation (ChIP)-sequencing experiments in lymphoid cells treated with the dietary isothiocyanate, sulforaphane (SFN) and carried out follow-up biological experiments on candidates. We found 242 high confidence, NRF2-bound genomic regions and 96% of these regions contained NRF2-regulatory sequence motifs. The majority of binding sites were near potential novel members of the NRF2 pathway. Validation of selected candidate genes using parallel ChIP techniques and in NRF2-silenced cell lines indicated that the expression of about two-thirds of the candidates are likely to be directly NRF2-dependent including retinoid X receptor alpha (RXRA). NRF2 regulation of RXRA has implications for response to retinoid treatments and adipogenesis. In mouse, 3T3-L1 cells' SFN treatment affected Rxra expression early in adipogenesis, and knockdown o...Continue Reading

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Datasets Mentioned

BETA
GSE37589
GM12878

Methods Mentioned

BETA
immunoprecipitation
ChIP
ChIP-seq
ChIP-PCR
transfection
ChIPseq
PCR

Software Mentioned

DAVID
- Alignment ( BWA ) Tool
Gibbs
Burrows
Ingenuity Pathway Analysis ( IPA )
Database for Annotation , Visualization and Integrated Discove...
QuEST
BWA

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