Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice

Background: The damaging effects of exposure to environmental toxicants differentially affect genetically distinct individuals, but the mechanisms contributing to these differences are poorly understood. Genetic variation affects the establishment of the gene regulatory landscape and thus gene expression, and we hypothesized that this contributes to the observed heterogeneity in individual responses to exogenous cellular insults. Objectives: We performed an in vivo study of how genetic variation and chromatin organization may dictate susceptibility to DNA damage, and influence the cellular response to such damage, caused by an environmental toxicant. Materials and Methods: We measured DNA damage, messenger RNA (mRNA) and microRNA (miRNA) expression, and genome-wide chromatin accessibility in lung tissue from two genetically divergent inbred mouse strains, C57BL/6J and CAST/EiJ, both in unexposed mice and in mice exposed to a model DNA-damaging chemical, 1,3-butadiene. Results: Our results showed that unexposed CAST/EiJ and C57BL/6J mice have very different chromatin organization and transcription profiles in the lung. Importantly, in unexposed CAST/EiJ mice, which acquired relatively less 1,3-butadiene-induced DNA damage, we observed increased transcription and a more accessible chromatin landscape around genes involved in detoxification pathways. Upon chemical exposure, chromatin was significantly remodeled in the lung of C57BL/6J mice, a strain that acquired higher levels of 1,3-butadiene–induced DNA damage, around the same genes, ultimately resembling the molecular profile of CAST/EiJ. Conclusions: These results suggest that strain-specific changes in chromatin and transcription in response to chemical exposure lead to a “compensation” for underlying genetic-driven interindividual differences in the baseline chromatin and transcriptional state. This work represents an example of how chemical and environmental exposures can be evaluated to better understand gene-by-environment interactions, and it demonstrates the important role of chromatin response in transcriptomic changes and, potentially, in deleterious effects of exposure. https://doi.org/10.1289/EHP1937


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. Air concentration of 1,3-butadiene inside the inhalation chamber. Data are presented as mean±SD. Figure S2. MA plot showing the average expression level and fold-change of each gene in CAST/EiJ control relative to C57BL/6J control. Genes with significantly higher expression in CAST/EiJ relative to C57BL/6J at an FDR of 10% are green, whereas genes with significantly higher expression in C57BL/6J relative to CAST/EiJ at an FDR of 10% are blue. Nonsignificant genes are in gray. Figure S3. Motif enrichments in differentially accessible regions (DARs) in clean air-exposed CAST/EiJ relative to C57BL/6J. Figure S4. MA plot showing the average expression level and fold-change of each gene in CAST/EiJ control relative to CAST/EiJ exposed to 1,3-butadiene (BD). Genes with significantly higher expression in CAST/EiJ control relative to CAST/EiJ exposed at an FDR of 10% are green, whereas genes with significantly higher expression in CAST/EiJ exposed relative to CAST/EiJ control at an FDR of 10% are orange. Nonsignificant genes are in gray. Figure S5. MA plot showing the average expression level and fold-change of each gene in C57BL/6J control relative to C57BL/6J exposed to 1,3-butadiene (BD). Genes with significantly higher expression in C57BL/6J control relative to C57BL/6J exposed at an FDR of 10% are blue, whereas genes with significantly higher expression in C57BL/6J exposed relative to C57BL/6J control at an FDR of 10% are red. Nonsignificant genes are in gray. Figure S6. Motif enrichments in differentially accessible regions (DARs) in 1,3-butadieneexposed mice C57BL/6J relative to clean air-exposed control mice. Figure S7. Chromatin accessibility and target gene expression at distal regions containing the Sp1 motif (A) On average, distal regions containing the Sp1 motif decrease in chromatin accessibility following 1,3-butadiene (BD) exposure in C57BL/6J to more closely resemble those regions in CAST/EiJ. (B) Similarly, genes associated with these regions also decrease in expression following BD exposure in C57BL/6J. Table S1. Sequencing statistics. Table S2. Differential mRNA expression analysis results, as determined by DESeq2. Table S3. Pathway enrichment based on gene expression profiles in the lung of CAST/EiJ mice exposed to clean air compared to that of C57BL/6J mice, using GSAA and the REACTOME database. Table S4. Differential miRNA expression analysis results, as determined by DESeq2, and denotation of master regulators of mRNA expression as determined by miRhub analysis. Table S5. Differential ATAC-seq chromatin accessibility analysis results, as determined by DESeq2. Table S6. Pathway enrichment based on chromatin accessibility profiles in the lung of CAST/EiJ mice exposed to clean air compared to that of C57BL/6J mice exposed to clean air, using GSAA and the REACTOME database. Table S7. Pathway enrichment based on gene expression profiles in the lung of CAST/EiJ mice exposed to 1,3-butadiene compared to that of CAST/EiJ mice exposed to clean air, using GSAA and the REACTOME database. Table S8. Pathway enrichment based on gene expression profiles in the lung of C57BL/6J mice exposed to 1,3-butadiene compared to that of C57BL/6J mice exposed to clean air, using GSAA and the REACTOME database. Table S9. Geneset enrichment based on 719 genes linked to one of the 2,188 proximal SP1containing DARs between C57BL/6J and CAST/EiJ at baseline, using GSAA and the REACTOME database. Table S10. Pathway enrichment based on differentially expressed genes and/or differentially accessible regions (DARs) in the lung of C57BL/6J mice exposed to 1,3 butadiene compared to C57BL/6J mice exposed to clean air, grouped by their patterns of expression/accessibility across both strains and conditions (Figure 5). Genes with significantly higher expression in CAST/EiJ relative to C57BL/6J at an FDR of 10% are green, whereas genes with significantly higher expression in C57BL/6J relative to CAST/EiJ at an FDR of 10% are blue. Nonsignificant genes are in gray. Figure S3. Motif enrichments in differentially accessible regions (DARs) in clean airexposed CAST/EiJ relative to C57BL/6J. Figure S4. MA plot showing the average expression level and fold-change of each gene in CAST/EiJ control relative to CAST/EiJ exposed to 1,3-butadiene (BD). Genes with significantly higher expression in CAST/EiJ control relative to CAST/EiJ exposed at an FDR of 10% are green, whereas genes with significantly higher expression in CAST/EiJ exposed relative to CAST/EiJ control at an FDR of 10% are orange. Nonsignificant genes are in gray. Figure S5. MA plot showing the average expression level and fold-change of each gene in C57BL/6J control relative to C57BL/6J exposed to 1,3-butadiene (BD). Genes with significantly higher expression in C57BL/6J control relative to C57BL/6J exposed at an FDR of 10% are blue, whereas genes with significantly higher expression in C57BL/6J exposed relative to C57BL/6J control at an FDR of 10% are red. Nonsignificant genes are in gray. Figure S6. Motif enrichments in differentially accessible regions (DARs) in 1,3butadiene-exposed mice C57BL/6J relative to clean air-exposed control mice. Figure S7. Chromatin accessibility and target gene expression at distal regions containing the Sp1 motif (A) On average, distal regions containing the Sp1 motif decrease in chromatin accessibility following 1,3-butadiene (BD) exposure in C57BL/6J to more closely resemble those regions in CAST/EiJ. (B) Similarly, genes associated with these regions also decrease in expression following BD exposure in C57BL/6J. Table S1. Sequencing statistics.

Excel
Excel Table S2. Differential mRNA expression analysis results, as determined by DESeq2.
Excel Table S3. Pathway enrichment based on gene expression profiles in the lung of CAST/EiJ mice exposed to clean air compared to that of C57BL/6J mice, using GSAA and the REACTOME database.
Excel Table S4. Differential miRNA expression analysis results, as determined by DESeq2, and denotation of master regulators of mRNA expression as determined by miRhub analysis.
Excel Table S5. Differential ATAC-seq chromatin accessibility analysis results, as determined by DESeq2.
Excel Table S6. Pathway enrichment based on chromatin accessibility profiles in the lung of CAST/EiJ mice exposed to clean air compared to that of C57BL/6J mice exposed to clean air, using GSAA and the REACTOME database.
Excel Table S7. Pathway enrichment based on gene expression profiles in the lung of CAST/EiJ mice exposed to 1,3-butadiene compared to that of CAST/EiJ mice exposed to clean air, using GSAA and the REACTOME database.
Excel Table S8. Pathway enrichment based on gene expression profiles in the lung of C57BL/6J mice exposed to 1,3-butadiene compared to that of C57BL/6J mice exposed to clean air, using GSAA and the REACTOME database.
Excel Table S9. Geneset enrichment based on 719 genes linked to one of the 2,188 proximal SP1-containing DARs between C57BL/6J and CAST/EiJ at baseline, using GSAA and the REACTOME database.
Excel Table S10. Pathway enrichment based on differentially expressed genes and/or differentially accessible regions (DARs) in the lung of C57BL/6J mice exposed to 1,3 butadiene compared to C57BL/6J mice exposed to clean air, grouped by their patterns of expression/accessibility across both strains and conditions (Figure 5).