What the interphase genome looks like in vivo is unknown. Advances in sequencing over the last decade have provided new insight into sequence variants (and their expression); yet how the genome is organized in three dimensions, apart from the well-described machinations of mitosis, is only beginning to be understood. Adult cardiac myocytes reside primarily in interphase but are capable of large-scale changes in gene expression. Transcription factors, histone modifying enzymes and RNA polymerase complexes play a central role in the process of global gene expression; however, an equally important and less explored factor is endogenous chromatin structure. To be transcribed, a gene's local environment must be accessible for protein binding. The objective of this grant is to understand how this phenomenon is integrated on a genome- wide scale: how is the genome appropriately poised to have the right genes on and off under basal conditions, and what are the mechanisms that globally reorganize chromatin following a stimulus (e.g. during disease)? Heart failure involves large-scale gene expression changes, including reactivation of genes normally silenced during development. Our data from an in vivo mouse model of pressure overload show alterations in abundance and localization of chromatin structural proteins from the linker histone H1 and high mobility group (HMG) B families, and indicate that heart failure is associated with global reprogramming of the chromatin environment for gene activation. We seek to discover universal principles for how HMGs and linker histones control bulk chromatin rearrangement and global gene expression; therefore, we will employ zebrafish, isolated myocytes and mouse hearts as model systems. Our unifying hypothesis is that global reorganization of chromatin structure during heart failure is the result of systematic changes in the abundance, genomic localization, and protein interactions among chromatin structural proteins. We will examine how linker histones and HMGs establish the higher order structure of the genome in the cardiac nucleus and how they dynamically repackage chromatin in disease. We will use gain/loss-of-function approaches combined with super resolution STED microscopy (image chromatin packing), chromatin immunoprecipitation and DNA sequencing (localize proteins across the genome) and proteomics (determine proteins necessary for targeting). Our short-term goal is to understand the role of HMGs and linker histones in cardiac phenotype. The long-term goal is to develop an understanding of how HMGs, linker histones and other chromatin structural proteins coordinate genomic structure to facilitate specificity in gene expression. The significance in the basic realm is to develop an integrated model of chromatin packing. The significance to the clinical realm is to provide a mechanistic basis for how the genome is reprogrammed with disease, such that future therapies can target specific chromatin remodeling events.
Fundamentally new strategies are needed to understand how the genome contributes to the human health problem of cardiovascular disease. We propose a novel systems approach combining chromatin immunoprecipitation plus DNA sequencing, super resolution microscopy and proteomics to examine chromatin structure in the setting of heart disease (in cells and mice) and development (in zebrafish). Our studies will test the hypothesis that genome-wide changes in gene expression are controlled by alterations in chromatin structural proteins, will reveal the principles underlying this phenomenon and have the potential to establish a new paradigm for how genomic structure affects cardiac phenotype during health and disease.
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