Nucleolar Proteins Controlling Cardiac Phenotype in Rat Myocytes and Zebrafish Revealed by Chromatin Proteomics

Cardiac hypertrophy is a common precursor to heart failure, during which cardiomyocytes grow to compensate for an increased workload. Hypertrophic cardiomyocytes undergo significant changes in cellular plasticity by adopting the expression profile and some phenotypic aspects of more primitive (embryonic or fetal) cardiac cells. These global changes in gene expression, conserved between humans and animal models of heart failure, must be preceded by structural alterations to the chromatin. Specifically, chromatin regions must be architecturally modified to allow or deny access for transcriptional machinery. However, the proteins responsible for remodeling chromatin to accomplish these gene expression changes during cardiac hypertrophy and failure are largely unknown. We used a proteomics approach to identify proteins bound to cardiac chromatin and to quantify changes in their abundance during disease. Quantitative mass spectrometry and bioinformatics revealed that 366 of the chromatin-bound proteins detected in this study displayed altered expression in a mouse model of pressure overload cardiac hypertrophy and failure. This included the chromatin remodeling protein Nucleolin (Ncl), which exhibited increased association with chromatin in the hypertrophic heart. To examine its role in regulating cardiac morphology and function we performed morpholino based knockdown of Ncl in zebrafish embryos. Ncl knockdown promoted the expression of bmp4 (a fetal marker), inhibited normal cardiomyocyte differentiation and resulted in abnormal heart chamber formation and looping. Hearts in surviving fish exhibited functional deficits as measured by fluorescence imaging and line-scanning analysis. To investigate the actions of Ncl in the mammalian cardiomyocyte, knockdown was carried out in isolated rat ventricular myocytes using siRNA. Loss of Ncl induced heterochromatin formation (increased Histone H3 K9-trimethylation), suppressed rDNA transcription (52% decrease in pre-rRNA via qPCR) and promoted fetal gene expression (65% increase in ANF; 41% increase in β-MHC transcripts). Overall, this study identifies Ncl as a regulator of chromatin structure, cell growth via ribosome biogenesis and cellular plasticity in the cardiomyocyte.