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.

• Authors: Nicholas J Lodato, Andy Rampersaud, David J Waxman
• Journal: Toxicological sciences : an official journal of the Society of Toxicology (Toxicol Sci) Vol. 164 Issue 1 Pg. 115-128 (07 01 2018) ISSN: 1096-0929 [Electronic] United States
• PMID: 29617930 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• Constitutive Androstane Receptor
• Ligands
• Nr1i3 protein, mouse
• Pyridines
• RNA, Long Noncoding
• Receptors, Cytoplasmic and Nuclear
• 1,4-bis(2-(3,5-dichloropyridyloxy))benzene

Topics

• Animals
• Chromatin Assembly and Disassembly (drug effects, genetics)
• Constitutive Androstane Receptor
• Female
• Gene Expression Regulation (drug effects)
• Ligands
• Liver (drug effects, metabolism)
• Male
• Mice, Inbred Strains
• Promoter Regions, Genetic
• Pyridines (toxicity)
• RNA, Long Noncoding (genetics)
• Receptors, Cytoplasmic and Nuclear (agonists, genetics)
• Sex Factors