The Effects of Sequence Variation on Genome-wide NRF2 Binding—New Target Genes and Regulatory SNPs

Abstract

Transcription factor binding specificity is crucial for proper target gene regulation. Motif discovery algorithms identify the main features of the binding patterns, but the accuracy on the lower affinity sites is often poor. Nuclear factor E2-related factor 2 (NRF2) is a ubiquitous redox-activated transcription factor having a key protective role against endogenous and exogenous oxidant and electrophile stress. Herein, we decipher the effects of sequence variation on the DNA binding sequence of NRF2, in order to identify both genome-wide binding sites for NRF2 and disease-associated regulatory SNPs (rSNPs) with drastic effects on NRF2 binding. Interactions between NRF2 and DNA were studied using molecular modelling, and NRF2 chromatin immunoprecipitation-sequence datasets together with protein binding microarray measurements were utilized to study binding sequence variation in detail. The binding model thus generated was used to identify genome-wide binding sites for NRF2, and genomic binding sites with rSNPs that have strong effects on NRF2 binding and reside on active regulatory elements in human cells. As a proof of concept, miR-126–3p and -5p were identified as NRF2 target microRNAs, and a rSNP (rs113067944) residing on NRF2 target gene (Ferritin, light polypeptide, FTL) promoter was experimentally verified to decrease NRF2 binding and result in decreased transcriptional activity.

Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer

“…According to the GWAS catalog (http://www.ebi.ac.uk/gwas/), six SNPs (rs9533090, rs9594738, rs17638544, rs8001611, rs9533095, and rs9594759) at 13q14.11 have been reported by previous GWASs on osteoporosis . These SNPs were located in the intergenic region close to AKAP11 (∼65 kb) and distal from RANKL (∼185 kb).…”

“…Multiple intergenic SNPs at 13q14.11 have been reported by previous GWASs on osteoporosis . Deciphering the functional mechanisms of how these noncoding SNPs influence osteoporosis risk is critical to help translate GWAS findings into clinically useful information.…”

“…Until now, several powerful genomewide association studies (GWASs) have identified multiple significant single‐nucleotide polymorphisms (SNPs) near RANKL at 13q14.11 for osteoporosis . However, these SNPs are all located in the intergenic region over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 .…”

Epigenetic Programming of Cardiovascular Disease by Perinatal Hypoxia and Fetal Growth Restriction

“…MiR-126 is encoded in the seventh intron of the gene for the endothelial-specific protein epidermal growth factor-like domain 7 (Egfl7) and its expression is partially (~30%) dependent on transcription factors that bind to the promoter region of this Egfl7 [93]. Additionally, miR-126 expression is regulated, independently of Egfl7, by the DNA methylation status of a miR-126-specific promoter located in intron 7 of Egfl7 [94], as well as the binding of Nrf2 to this region in response to oxidative stress [95]. Preliminary data from our group show that FGR human endothelial cells present increased levels of DNA methylation in miR-126 promoter, suggesting an epigenetic programming of this miRNA in FGR endothelium.…”

Divergence and rewiring of regulatory networks for neural development between human and other species

“…Mutations in TF binding sites, including point mutations and indels, can explain a substantial portion but not all of the binding divergence. [25][26][27] Despite the dramatic turnover of individual TF binding, Ballester et al found that about 2-thirds of TF binding sites were located within cis-regulatory modules (CRMs), although less than half of the CRMs in humans were also CRMs in other species, 28 suggesting some degree of coevolution of different TF binding.…”