title: Identification of novel NRF2-regulated genes by ChIP-Seq: influence on retinoid X receptor alpha.
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 of Nrf2-delayed Rxra expression, both leading to impaired adipogenesis.
authors.affiliation: Environmental Genomics Section, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: Brian N
authors.initials: BN
authors.lastname: Chorley
authors.forename: Michelle R
authors.initials: MR
authors.lastname: Campbell
authors.forename: Xuting
authors.initials: X
authors.lastname: Wang
authors.forename: Mehmet
authors.initials: M
authors.lastname: Karaca
authors.forename: Deepa
authors.initials: D
authors.lastname: Sambandan
authors.forename: Fatu
authors.initials: F
authors.lastname: Bangura
authors.forename: Peng
authors.initials: P
authors.lastname: Xue
authors.forename: Jingbo
authors.initials: J
authors.lastname: Pi
authors.forename: Steven R
authors.initials: SR
authors.lastname: Kleeberger
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Bell
mesh_terms: D041721:3T3-L1 Cells; D017667:Adipocytes / Q000166:cytology / Q000378:metabolism; D050156:Adipogenesis; D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D017879:Isothiocyanates; D008214:Lymphocytes / Q000187:drug effects / Q000378:metabolism; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D050983:NF-E2 Transcription Factor / Q000378:metabolism; D051267:NF-E2-Related Factor 2 / Q000378:metabolism*; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D020218:Response Elements; D047490:Retinoid X Receptor alpha / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D013454:Sulfoxides; D013861:Thiocyanates / Q000494:pharmacology
chemical_list: D017879:Isothiocyanates; D035683:MicroRNAs; D050983:NF-E2 Transcription Factor; D051267:NF-E2-Related Factor 2; C495635:NFE2L2 protein, human; C495636:Nfe2l2 protein, mouse; D047490:Retinoid X Receptor alpha; D013454:Sulfoxides; D013861:Thiocyanates; C016766:sulforaphane