Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

Abstract

The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1−/−) or depletion (Nrf2−/−) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response.

The NRF2‐related interactome and regulome contain multifunctional proteins and fine‐tuned autoregulatory loops

“…To predict target genes regulated by NRF2, we applied the transcription factor binding site (TFBS) information of NRF2 from JASPAR [17]. We also included all experimentally verified NRF2 target genes from a large-scale ChIP-Seq profiling study [10]. In order to predict transcription factors (TFs) that directly regulate NRF2 transcription, we applied a reverse approach, and queried the regulatory region of the NRF2 gene sequence against all TFBS information found in JASPAR [17].…”

“…First, by manual curation we found 29 NRF2 target genes in the literature. We extended this list by including 6 target genes from the manually curated InnateDB and 1054 genes identified in a large-scale ChIP-Seq study [10]. Based on TF-TFBS binding data from JASPAR [17], we further predicted 6426 NRF2 target genes.…”

“…The small overlap among the sources, especially between the large-scale ChIP-Seq study and the JASPAR prediction was surprising but can be explained by checking the details of these methods. The examined sequence regions were much broader in the prediction (see Supplementary Material 1) and the ChIP-Seq study contained only confident, functional and NRF2-specific target sequences [10]. Thus, the prediction may contain non-functional NRF2 binding sites but it may also list those binding sites that are bound by NRF2 in complex with other transcription factors containing homeodomain or bZIP domains.…”

“…While there are more than 2300 articles for the keyword 'NRF2' in PubMed (as of January 2012), major protein-protein interaction resources (BioGRID, MINT, STRING, HPRD) contain only a few (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) interactors for NRF2. Besides one study on the global mapping of binding sites for NRF2 through ChIP-Seq profiling [10] and a specific network modeling approach on Nrf2 regulation in mouse lung [11], there is no large-scale collection of NRF2-regulated target genes. Prompted by the lack of systems-level NRF2-related information we collected literature information on NRF2 interacting proteins and regulated genes, as well as predicted novel NRF2 interactors and regulators.…”

La voie Nrf2 en pathologie respiratoire

“…La réponse au stress utilisant la voie de signalisation Nrf2/Keap1-Bach1 est impliquée dans la protection contre le vieillissement, la neurodégénérescence, la carcinogenèse, l'hépatotoxicité, les maladies cardiovasculaires et les maladies respiratoires comme la bronchopneumopathie chronique obstructive (BPCO) et l'emphysème, l'asthme, la fibrose et les agressions pulmonaires aiguës [12]. En pathologie respiratoire, des études récentes ont confirmé chez l'homme les résultats obtenus dans les modèles animaux.…”