GSE109012
CHD4 and the NuRD complex directly control cardiac sarcomere formation
Cardiac development relies on proper cardiomyocyte differentiation including expression and assembly of cell-type specific actomyosin subunits into a functional cardiac sarcomere. Control of this process involves not only promoting expression of cardiac sarcomere subunits but also repressing expression of non-cardiac myofibril paralogs. This level of transcriptional control requires broadly expressed multiprotein machines that modify and remodel the chromatin landscape to restrict transcription machinery access. Prominent among these is the Nucleosome Remodeling and Deacetylase (NuRD) complex, which includes the catalytic core subunit CHD4. Here, we demonstrate that direct CHD4-mediated repression of skeletal and smooth muscle myofibril isoforms is required for normal cardiac sarcomere formation, function, and embryonic survival early in gestation. Through transcriptomic and system genome-wide analyses of CHD4 localization, we identified novel CHD4 binding sites in smooth muscle myosin heavy chain, fast skeletal a-actin, and the fast skeletal troponin complex genes. We further demonstrate that in the absence of CHD4, cardiomyocytes in the developing heart form a hybrid muscle cell that contains cardiac, skeletal and smooth muscle myofibril components. These misexpressed paralogs intercalate into the nascent cardiac sarcomere to disrupt sarcomere formation and cause impaired cardiac function in utero. These results demonstrate the genomic and physiological requirements for CHD4 in mammalian cardiac development. Overall design: mRNA profiles from cardiac tissue of 3 biological replicates of control Chd4flox/flox or CHD4-depleted Chd4?flox/?flox at E10.5 and 5 biological replicates of control Chd4flox/flox  or CHD4-depleted Chd4?flox/?flox at E9.5 were generated by high-throughput sequencing for transcriptome analysis. CHD4-bound genomic DNA from E10.0 cardiac tissue (2 biological replicates, 3 technical replicates from wild-type embryos) was isolated and sequenced for genomic localization analysis.