Abstract 10470: Nucleosome Positioning is a Mechanism of Global Chromatin Structural Remodeling in Cardiac Hypertrophy
The re-expression of fetal cardiac genes during disease requires coordinated chromatin remodeling. Local chromatin packing around the nucleosome protein complex is understood with atomic resolution; however, higher level properties of chromatin packing in the cardiovascular system are unknown. We hypothesized that nucleosome occupancy (i.e. exact positioning of nucleosomes at given loci) is a feature that regulates altered gene expression in hypertrophy. To investigate mechanisms that establish chromatin structure, genome-wide nucleosome location in heart was determined by Micrococcal Nuclease treatment followed by next-generation sequencing (MNase-Seq). A total of 137.4M Illumina reads were acquired from normal and hypertrophic myocardium, and Novoalign used to align them to the mouse genome mm9 with an average mapping percentage of 59%. Resulting occupancy profiles from normal and diseased cardiac myocytes exhibit global (i.e. chromosome scale) similarities, but local (i.e. gene/promoter scale) differences. These findings support that primary DNA sequence can specify nucleosome localization globally (evinced by correlation between GC content and nucleosome occupancy), whereas local changes during disease imply dynamic mechanisms that are sequence-independent. Specifically, different occupancy patterns were observed in the promoter regions of genes altered in hypertrophy (including alpha and beta myosin heavy chain). Because the average length of linker DNA (i.e. segment between two nucleosomes) fundamentally contributes to chromatin compaction, we measured this parameter by limited MNase digestion. The findings demonstrate that linker DNA length, and therefore nucleosome density, differs between cell types and is altered in the setting of hypertrophy. To examine a subset of nucleosomes involved in specific gene regulatory events, chromatin immunoprecipitation was performed for histone H2A.z and other chromatin structural proteins. Coupled with DNA sequencing, these studies reveal specific genes targeted by these chromatin structural proteins. These findings are the first to demonstrate nucleosome remodeling as a dynamic process in the heart, capable of global changes in gene expression during disease.
- © 2011 by American Heart Association, Inc.