Regulation of mouse liver chromatin accessibility and associated early gene responses by CAR

Abstract

Many xenobiotics are metabolized in mammalian liver by pathways regulated by constitutive androstane receptor (CAR). Here, we identify early gene targets of mouse liver CAR and investigate their associated, CAR‐induced changes in local chromatin accessibility and transcription factor (TF) recruitment. Genes induced or repressed by the CAR agonist TCPOBOP were identified by RNA‐Seq after 3 or 27 hr. Chromatin sites that dynamically open or close following CAR activation (changes in DNase I hypersensitive sites, ΔDHS) were identified by DNase‐Seq. Genes dysregulated in 3 hr TCPOBOP‐treated mouse liver were enriched in KEGG pathways for retinol and drug metabolism (DAVID analysis; p<E‐15). IPA identified activated CAR and its agonists as the top predicted upstream regulators of these gene responses. After 27 hr TCPOBOP treatment, many more genes were identified and the predicted upstream regulators expanded to include cyclin D and vitamin D, indicating significant secondary transcriptional regulation. DNase‐Seq identified ~3,600 ΔDHS that were opened or closed by 3 hr TCPOBOP treatment. These ΔDHS were not randomly distributed: mapping to their putative gene targets (i.e., nearest gene within 10 kb) revealed enrichment (12.4‐fold, p<E‐45) of the TCPOBOP‐induced DHS for genes inducible by CAR. Thus, chromatin opening is associated with activation of nearby CAR target genes. Genomic sequences in the 3 hr TCPOBOP‐inducible DHS regions were enriched for TF binding motifs for CAR and for CCAAT‐enhancer binding protein (CEBP), suggesting that CEBPs cooperate with CAR to open chromatin and up regulate target gene expression. Studies designed to test this hypothesis are in progress and will be reported. Grant support: NIH ES024421.