Abstract 19076: ATAC-seq Implicates Epigenome-wide CTCF Dissociation in the Progression of Cardiac Ischemia

Abstract

Introduction: Heart disease is currently the most common cause of death in the United States. In 2010 alone, over 375,000 people died of coronary heart disease, of which over 120,000 were from myocardial infarction. Due to technical challenges associated with current techniques, profiling epigenome changes due to myocardial infarction has been limited. We have optimized an assay for transposase-accessible chromatin with sequencing (ATAC-seq) protocol that circumvents these challenges and works well with frozen tissue. Hypothesis: We assessed the hypothesis that ATAC-seq would enable the identification of novel chromatin remodeling and transcription factor binding events in a murine model of cardiac ischemia. Methods: Six 10 ± 2 week old C57BL/6J mice were paired by same gender, age, and litter, and mice from these pairs were selected for either mid left anterior descending artery ligation or sham surgery, both for 30 minutes. Successful ligation was confirmed by blanching of the tissue and representative electrocardiography changes. We performed our ATAC-seq protocol on left ventricular tissues, and regions of open chromatin were determined using the Hotspot algorithm at a false detection rate of 0.5%. Gene ontology was performed with the Genomic Regions Enrichment of Annotations Tool (GREAT), and motif discovery was performed with the Multiple Em for Motif Elicitation (MEME) Suite. Results: From stringent overlap criteria were obtained 159 loci that became “open” due to ischemia and 782 loci that became “closed”. Downregulation of growth and signaling processes was determined by GREAT. MEME strongly implicated the dissociation of CCCTC-binding Factor (CTCF) due to ischemia (MEME E-score = 8.10e-235; motif identification p -value = 1.88e-18; 262/782 of “closed” loci). CTCF ChIP-seq data and footprint analysis enabled the further identification of a robust set of 189 CTCF differential binding events. Conclusions: ATAC-seq was able to identify widespread chromatin remodeling due to cardiac ischemia alone. We identified a robust set of 189 gene loci from which CTCF binding is attenuated in response to this disease state. To our knowledge, this represents the first study that has examined chromatin accessibility changes in the setting of cardiac ischemia.