Abstract 940: Global Analysis of Histone Modifications and Long-range Chromatin Interactions Revealed the Differential Cistrome Changes and Novel Transcriptional Players in Dilated Cardiomyopathy

Abstract

Background: Acetylation and methylation of histone alter the chromatin structure and accessibility that allows or prevents transcriptional regulators to bind to enhancers or promoters. The binding of transcriptional regulators enables the interaction between enhancers and promoters, thus affecting gene expression. However, our knowledge on the regulation of promoter and enhancer interactions and histone modifications in patients with heart failure remains limited. Methods and Results: We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) for major histone modifications and proximity ligation-assisted ChIP-seq (PLAC-seq) for long-range chromatin interaction for enhancer and promoter (E-P) using left ventricular tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors (n=2-3). We detected 37,531, and 8,587 differential H3K27ac and H3K4me3 regions between NF and DCM respectively (FDR <0.05). While the average read density (ARD) for H3K27ac, an active enhancer histone mark, is similar between NF and DCM, we observed the ARD of H3K4me3, which marks the active promoter region of the genes, is significantly lower in DCM samples than in NF ones (p<0.01). Super-enhancer (SE) analysis revealed that 481 and 119 genes are associated with NF- and DCM-specific SE respectively. Moreover, the differential E-P interactions were observed in the known heart failure gene loci, e.g., CTGF and NPPA-NPPB and these alternation interactions are correlated with the gene expression levels. Motif analysis identified known cardiac factors, such as MEF 2D and A and possible novel players, such as SOX transcription factors, namely SOX4 and SOX8, are enriched within enhancers and prompter regions identified in DCM samples. Their expression levels were confirmed with the whole-transcriptome analysis and protein assays. Conclusions: We have established cistrome for major histone modifications and long-range chromatin interaction for enhancer and promoter in NF and DCM tissues. The differential histone modifications and E-P interactions were found in DCM and these differences were associated with the gene expression level of a subset of disease-associated genes in human heart failure.