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.

A novel Nrf2-miR-29-desmocollin-2 axis regulates desmosome function in keratinocytes

“…Surprisingly, however, treatment of these lymphoblastoid cells with the NRF2-activating compound sulforaphane resulted in a downregulation of mature miR-29b (ref. 14). The discrepancy to our results obtained in keratinocytes may result from NRF2-independent effects of sulforaphane on expression/maturation of miR-29 (ref.…”

“…Another NRF2 ChIP-Seq study using human lymphoblastoid cells confirmed the genome-wide distribution of NRF2 binding in the vicinity of miRNA genes and found a peak of NRF2 binding in the upstream region of the human MIR29AB1 cluster 14 . Surprisingly, however, treatment of these lymphoblastoid cells with the NRF2-activating compound sulforaphane resulted in a downregulation of mature miR-29b (ref.…”

“…Rather, it also controls expression of genes with other functions, such as regulation of cell proliferation and survival 13 . Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) revealed that Nrf2 binds to promoters of genes encoding microRNAs (miRNAs, miRs) [13][14][15] , although the functional consequences remain largely unknown.…”

NRF2-driven miR-125B1 and miR-29B1 transcriptional regulation controls a novel anti-apoptotic miRNA regulatory network for AML survival

“…A recent study using chromatin immunoprecipitation sequencing (ChIP-Seq) identified high-confidence ChIP-Seq peaks for NRF2 binding in the vicinity of several miRNAs, suggesting they could be regulated by NRF2. 15 In the present study, we look to identify whether NRF2 regulates miRNA in human AML. Furthermore, we evaluate whether NRF2-regulated miRNAs have functional importance not only on the biology of the disease but also in the leukaemia cell death to chemotherapy treatment.…”

Multiple roles of Nrf2-Keap1 signaling

“…[19][20][21][22][23] Nrf2 can directly bind and activate adipogenic genes such as peroxisome proliferator-activated receptor γ (Pparγ) 21 and retinoid X receptor α (RXRA). 24 Nrf2 controls hematopoietic stem cell functions through transcriptional regulation of CXCR4. 22 In mouse liver, Nrf2 activates small heterodimer partner (SHP) nuclear receptor and lipid metabolism genes.…”