title: 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.
authors.affiliation: Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Suvi M
authors.initials: SM
authors.lastname: Kuosmanen
authors.affiliation: School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Sari
authors.initials: S
authors.lastname: Viitala
authors.affiliation: School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Tuomo
authors.initials: T
authors.lastname: Laitinen
authors.affiliation: School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Mikael
authors.initials: M
authors.lastname: Peräkylä
authors.affiliation: Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Petri
authors.initials: P
authors.lastname: Pölönen
authors.affiliation: Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Emilia
authors.initials: E
authors.lastname: Kansanen
authors.affiliation: Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Hanna
authors.initials: H
authors.lastname: Leinonen
authors.affiliation: Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Suresh
authors.initials: S
authors.lastname: Raju
authors.affiliation: Luxembourg Institute of Health, L-2160 Luxembourg, Luxembourg.
authors.forename: Anke
authors.initials: A
authors.lastname: Wienecke-Baldacchino
authors.affiliation: School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Ale
authors.initials: A
authors.lastname: Närvänen
authors.affiliation: School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Antti
authors.initials: A
authors.lastname: Poso
authors.affiliation: Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Merja
authors.initials: M
authors.lastname: Heinäniemi
authors.affiliation: Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland.
authors.forename: Sami
authors.identifier: http://orcid.org/0000-0002-6083-2402
authors.initials: S
authors.lastname: Heikkinen
authors.affiliation: Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland anna-liisa.levonen@uef.fi.
authors.forename: Anna-Liisa
authors.initials: AL
authors.lastname: Levonen
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D051267:NF-E2-Related Factor 2 / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014158:Transcription, Genetic
chemical_list: C527111:MIRN126 microRNA, human; D035683:MicroRNAs; D051267:NF-E2-Related Factor 2; C495635:NFE2L2 protein, human
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