Impact of CAR Agonist Ligand TCPOBOP on Mouse Liver Chromatin Accessibility

Abstract

Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1, 4-bis[2-(3, 5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long noncoding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions. We show that a subset of TCPOBOP-responsive genes cluster within TADs, and that TCPOBOP-induced genes and TCPOBOP-repressed genes are often found in different TADs. Further, using DNase-seq and DNase hypersensitivity site (DHS) analysis, we identified several thousand genomic regions (ΔDHS) where short-term exposure to TCPOBOP induces localized changes (increases or decreases) in mouse liver chromatin accessibility, many of which cluster in TADs together with TCPOBOP-responsive genes. Sites of chromatin opening were highly enriched nearby genes induced by TCPOBOP and chromatin closing was highly enriched nearby genes repressed by TCPOBOP, consistent with TCPOBOP-responsive ΔDHS serving as enhancers and promoters that positively regulate CAR-responsive genes. Gene expression changes lagged behind chromatin opening or closing for a subset of TCPOBOP-responsive ΔDHS. ΔDHS that were specifically responsive to TCPOBOP in male liver were significantly enriched for genomic regions with a basal male bias in chromatin accessibility; however, the male-biased response of hepatocellular carcinoma-related genes to TCPOBOP was not associated with a correspondingly male-biased ΔDHS response. These studies elucidate the genome-wide organization of CAR-responsive genes and of the thousands of associated genomic sites where TCPOBOP exposure induces both rapid and persistent changes in chromatin accessibility.

The Basis for Strain-Dependent Rat Aldehyde Dehydrogenase 1A7 (ALDH1A7) Gene Expression

“…These data correlate well with our findings on the RR ALDH1A7 gene. The murine Aldh1a7 locus contains an active promoter, as evidenced by activating histone H3K4me3 and H3K27Ac marks (Sugathan and Waxman, 2013) and a TCPOBOPresponsive DNase I hypersensitive site (Lodato et al, 2018) overlapping the TSS, a finding that matches well with the active rat ALDH1A7 proximal promoter in RR rats. The far-upstream DNase I hypersensitive sites are located at Fig.…”

Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2

“…50 nt paired-end sequence reads were obtained on an Illumina HiSeq instrument. ChIP-seq analysis was performed using a custom analysis pipeline initially developed for DNase-seq analysis and described elsewhere [48]. Individual biological replicates were validated using standard quality control metrics (FASTQC reports, confirmation of read length, and absence of read strand bias).…”

Health-Relevant Phenotypes in the Offspring of Mice Given CAR Activators Prior to Pregnancy

“…Mechanism. The latest literature suggests that persistent epigenetic changes in the promoters of CAR target genes, including Cyp2b10, are responsible for prolonged induction within the F0 generation in the liver (Chen et al, 2012;Peng and Zhong, 2015;Tien et al, 2015Tien et al, , 2017Li et al, 2016;Piekos et al, 2017;Lodato et al, 2018). Our work indicates that at least some of these effects may have been driven by activator accumulation rather than by stable DNA modifications.…”