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Impact of CAR Agonist Ligand TCPOBOP on Mouse Liver Chromatin Accessibility
Nicholas J Lodato1, Andy Rampersaud1, David J Waxman1
1Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215.
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.
Insights
Activation of the Constitutive Androstane Receptor (CAR) by TCPOBOP alters gene expression and chromatin accessibility in mouse liver. These CAR-induced changes are organized within topologically associating domains (TADs), influencing gene regulation and hepatocarcinogenesis.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- The Constitutive Androstane Receptor (CAR) is a nuclear receptor that regulates gene expression in the liver.
- CAR activation by TCPOBOP leads to widespread gene dysregulation and is implicated in male-biased hepatocarcinogenesis.
- Topologically associating domains (TADs) provide a structural framework for genome organization and enhancer-promoter interactions.
Purpose of the Study:
- To investigate the genomic organization of CAR-induced gene responses within TADs.
- To identify genomic regions with altered chromatin accessibility upon TCPOBOP exposure.
- To understand the relationship between chromatin changes, gene expression, and sex-biased responses.
Main Methods:
- Analysis of TCPOBOP-responsive RefSeq coding and long noncoding RNA (lncRNA) genes across TADs.
- DNase-seq and DNase hypersensitivity site (DHS) analysis to identify changes in chromatin accessibility (ΔDHS).
- Correlation of ΔDHS with TCPOBOP-responsive genes and assessment of sex-specific chromatin accessibility biases.
Main Results:
- TCPOBOP-responsive genes are frequently clustered within TADs, with induced and repressed genes often in separate TADs.
- Thousands of genomic regions (ΔDHS) showed altered chromatin accessibility upon TCPOBOP exposure, many within TADs containing responsive genes.
- Chromatin opening correlated with gene induction, and closing with repression, suggesting ΔDHS function as regulatory elements.
- Gene expression changes lagged behind chromatin accessibility alterations for some genes.
- Male-specific ΔDHS responses were enriched in regions with basal male chromatin accessibility bias, but this did not extend to male-biased hepatocellular carcinoma-related gene responses.
Conclusions:
- CAR-mediated gene regulation is organized within the TAD structure of the genome.
- TCPOBOP induces rapid and persistent changes in chromatin accessibility at thousands of genomic sites, acting as regulatory elements for CAR-responsive genes.
- While chromatin accessibility shows male bias in response to TCPOBOP, this does not fully explain the male-biased response of hepatocellular carcinoma-related genes.
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