Systems Proteomics of Cardiac Chromatin Identifies Nucleolin as a Regulator of Growth and Cellular Plasticity in Cardiomyocytes

Myocyte hypertrophy antecedent to heart failure involves changes in global gene expression, although the preceding mechanisms to coordinate DNA accessibility on a genomic scale are unknown. Chromatin-associated proteins can alter chromatin structure by changing their association with DNA, thereby altering the gene expression profile. Little is known about the global changes in chromatin sub-proteomes that accompany heart failure, and the mechanisms by which these proteins alter chromatin structure. The present study tests the fundamental hypothesis that cardiac growth and plasticity in the setting of disease recapitulates conserved developmental chromatin remodeling events. We used quantitative proteomics to identify chromatin-associated proteins extracted via detergent and to quantify changes in abundance during disease. Our study identified 321 proteins in this sub-proteome, demonstrating it to have modest conservation with that revealed using strong acid. Of these proteins, 176 exhibited altered expression during cardiac hypertrophy and failure; we conducted extensive functional characterization of one of these proteins, Nucleolin. Morpholino-based knockdown of nucleolin abolished protein expression but surprisingly had little impact on gross morphological development. However, zebrafish hearts lacking Nucleolin displayed severe developmental impairment, abnormal chamber patterning and functional deficits, ostensibly due to defects in cardiac looping and myocyte differentiation. The mechanisms underlying these defects involve perturbed BMP4 expression, decreased rRNA transcription and a shift to more heterochromatic chromatin. This study reports the quantitative analysis of a new chromatin sub-proteome in the normal and diseased mouse heart. Validation studies in zebrafish examine the role of Nucleolin to orchestrate genomic reprogramming events shared between development and disease.