Single nucleus multiome (GEX and ATAC) and bulk RNA-sq analysis of control and Mycn conditional knockout in the neonatal mouse heart

To investigate the role of MYCN in neonatal heart development, we performed Single nucleus multiome (GEX and ATAC) on isolated nuclei from control and Mycn conditional knockout (CKO) P4 mouse ventricles. Clustering analysis assigned cardiomyocytes (CMs) into five previously defined neonatal states (CM1–CM5). CKO hearts showed a marked depletion of proliferative CM2 and CM4 populations and an increase in differentiated CM1 cells. G2/M phase CMs were significantly reduced in the CKO, particularly within CM4. RNA velocity analysis revealed disrupted transitions from immature CM states to mature ones in the CKO. Latent time and metabolic profiling further confirmed a shift toward a mature, non-regenerative phenotype, with upregulation of hypertrophic and fatty acid oxidation pathways and downregulation of glycolysis and cell cycle genes. These results highlight MYCN’s role in maintaining proliferative, regenerative CM states during neonatal heart development. Bulk RNA-seq was performed on P30 mouse ventriclar tissue 28 days after ischemic injury to compare Mycn conditional knockout (CKO) and control groups. The analysis revealed that cell cycle and muscle development pathways were downregulated, while inflammatory pathways were upregulated in the Mycn CKO hearts. These findings suggest that MYCN is essential for maintaining proliferative and regenerative gene programs following cardiac injury, and its deletion impairs regenerative potential at the transcriptomic level.