Wilson disease: intersecting DNA methylation and histone acetylation mechanisms affect gene expression regulation in a mouse model of hepatic copper accumulation [ChIP-Seq]

Prior investigations of DNA methylation differences in WD liver and blood and in a WD mouse model revealed an epigenetic signature of WD that included the histone deacetylase, HDAC5. To test the hypothesis that histone deacetylation and acetylation might be altered with respect to copper overload and aberrant DNA methylation in WD, we used the Jackson Laboratory toxic milk model (tx-j) of WD to study the involvement of Class IIa histone deacetylases (HDAC4 and HDAC5) and histone acetylation (H3K9ac and H3K27ac), and the effects of copper chelator D-penicillamine (PCA) and/or methyl group donor choline on histone modification. Next, we related acetylation profiles of H3K27ac to gene expression changes in wilson disease by ChIP and RNA-seq. Overall design: Examination of histone modifications specifically H3K9-H3K27 acetylation enriched gene regulation in liver of WD mice models. Co-upregulated and downregulated genes with H3K27 acetylation and transcriptomes analysis (RNA-Seq) were identified to study the transcription factors and biological pathways involved in pathogenesis of WD. We demonstrate a role for histone deacetylases at the interface between nutrition, histone acetylation, DNA methylation, and gene expression regulation affecting liver disease severity in WD. Number of samples=70: 30 samples per H3K9ac and H3K27ac antibody and 2 input samples per treatment group. Experiment includes 6 sample per treatment group as 1: C3H-Wildtype, 2: tx-j- Untreated-Mutant (Atp7btx-J), 3: tx-j-PCA- Untreated tx-j+ Penicillamine (copper chelator), 4: tx-j+Choline- Untreated tx-j+ Choline (methyl group doner), 5: tx-j+PCA+Choline- Untreated tx-j+ both PCA and Choline.