Background: DNA methylation and hydroxymethylation plays critical role in important biological processes, including differentiation of tissues in the embryo and cellular response to different diseases and diverse environmental factors. The epigenetic landscape in heart failure might be altered.
Purpose: Our objective was to determine how Mybpc3 deficiency, which produces hypertrophic cardiomyopathy, affects epigenetic landscape, gene expression, and regulation.
Methods: We generated and analysed genome-wide DNA methylomes and hydroxymethylomes from cardiac tissues of 12-week old Mybpc3−/− mice and littermate controls, and performed whole genome RNA sequencing (RNA-seq) for gene expression and validated the findings using qPCR.
Results: Single base resolution revealed overall lower 5-mC level in Mybpc3 deficient mice. In deficient mice, different genic regions including transcription start site, exons, and introns, had low levels of 5-mC. Although there was no overall difference in 5-hmC content, knockout mice had lower levels of 5-hmC in the distal part of the genes (last exon, transcription termination site, and 3'-flanking regions). The 5-hmC enrichment in the intronic regions was associated with higher gene expression, whereas, the presence of 5-mC in the 5'-flanking regions was associated with lower gene expression in both knockout and wildtype mice. Ingenuity pathway analysis (IPA) of differentially expressed genes revealed overrepresentation of genes involved in axonal-guidance pathway. Tet activity was downregulated in Mybpc3−/− mice, and it may explain the overall difference of 5-mC in deficient mice. We also observed that Mybpc3 ablation affected alternative splicing of Myh6 and Myh7.
Conclusion: This study establishes that knocking out of Mybpc3 changes epigenetic landscape in cardiac tissue, which is tightly linked to gene expression and regulation.