Abstract 355: Systems Epigenomics of Chromatin Structure in the Heart

Abstract

Except during metaphase, endogenous chromatin structure is unknown. DNA - invariant between cells - and the cell type-specific modifiers of the genome establish chromatin structural features, both local (e.g. at the scale of individual nucleosomes) and global (e.g. chromosomal territories). A fundamental question is how these cell type-specific modifiers, including DNA modification, non-coding RNAs, and proteins, establish the chromatin environment conducive to gene expression for the correct cell type: in cardiac muscle, how is the genome structurally poised to confer cardiac (and not, say, renal) transcriptomes and proteomes, and what physical reprogramming events occur during disease? To address these questions, we are conducting a systems analysis of the epigenetic features of the healthy and diseased heart. In adult mice, we have used quantitative mass spectrometry to dissect distinct fractions of the nucleus and reveal the itineraries of chromatin structural proteins, enzymatic nucleosome remodelers, histone molecules and histone post-translational modifications. These studies have revealed rules for global reprogramming of gene expression, which involve altered abundance of non-histone chromatin structural proteins, a shift from hetero- towards euchromatic post-translational marks and a decreased linker to core histone ratio in heart failure. Furthermore, interrogation of genome-wide binding patterns of known cardiac transcription factors within the genes that encode proteins operative in cardiac genomic structure reveals hierarchical relationships between these protein, transcript and gene networks. Complementary investigations in isolated myocytes are characterizing the global rearrangement of chromatin following hypertrophic agonist treatment using conventional and super-resolution microscopy to directly visualize the chromatin backbone. Lastly, a combination of multiple genomic scale sequencing studies have revealed regions under control of specific chromatin structural proteins. Together, these studies aim to address the basic question of how global chromatin structure is maintained in cardiac myocytes and how diseases like heart failure result from deranged chromatin structure on a genomic scale.