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

Nucleic Acids Res. 2012 Aug;40(15):7416-29. doi: 10.1093/nar/gks409. Epub 2012 May 11.

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.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • 3T3-L1 Cells
  • Adipocytes / cytology
  • Adipocytes / metabolism
  • Adipogenesis
  • Animals
  • Binding Sites
  • Cell Line
  • Cells, Cultured
  • Chromatin Immunoprecipitation
  • Gene Expression Regulation*
  • Genome, Human
  • Humans
  • Isothiocyanates
  • Lymphocytes / drug effects
  • Lymphocytes / metabolism
  • Mice
  • MicroRNAs / metabolism
  • NF-E2 Transcription Factor / metabolism
  • NF-E2-Related Factor 2 / metabolism*
  • Nucleotide Motifs
  • Promoter Regions, Genetic
  • Response Elements
  • Retinoid X Receptor alpha / metabolism*
  • Sequence Analysis, DNA
  • Thiocyanates / pharmacology

Substances

  • Isothiocyanates
  • MicroRNAs
  • NF-E2 Transcription Factor
  • NF-E2-Related Factor 2
  • NFE2L2 protein, human
  • Nfe2l2 protein, mouse
  • Retinoid X Receptor alpha
  • Thiocyanates
  • sulforaphane