Neonatal Mouse Heart Maturation: Transcriptome-Wide Analysis Reveals Chamber-Specific Exon Enrichment of Cell Cycle Genes

Background: During postnatal maturation of mammalian heart the neonatal cardiomyocytes undergo dramatic changes including complete maturation, proliferation arrest, and terminal exit from the cell cycle (CC). However, transcriptome-wide analysis of CC programs has not been performed in perinatal stages among different cardiac chambers. In particular, the contribution of alternative RNA splicing to the chamber-specific CC activities is unexplored Design/Methods: To achieve comprehensive analysis of differential expression (DE) and alternative splicing (AS) of CC-related genes in left ventricle (LV) versus right ventricle (RV) during maturation deep RNA-seq was performed on male newborn mouse LV and RV at 3 time points of perinatal transition: P0, P3 and P7. Reads were mapped to mouse Transcriptome, and to mouse Genome. Transcriptome-Wide difference in inclusion of individual exons was performed using MATS. DE genes and AS variants were defined as those with fold change ≥2, at expression level ≥3 RBKM and a false discovery rate ≤0.05. Significant gene ontology (GO) terms were determined at P-value ≤0.05. Levels of expression were validated using qRT-PCR Results: Altogether, 2116 DE genes and 1162 AS events were observed. Among them, 109 CC-related genes were further analyzed. Distinct temporal patterns of DE and GO enrichment of CC genes in LV vs. RV during maturation were identified. Chamber -specific induction of genes involved in mitosis, karyokinesis, and cytokinesis was found at P7. RNA Splicing analysis of CC genes revealed 77 AS events. Skipping exon accounted for nearly half splicing events. Among 30 spliced exon variants, significant chamber-and temporal-specific inclusion were observed. Interestingly, the majority of AS variants exhibited opposing patterns of exon usage in RV vs. LV at p7 Conclusions: Our findings suggest novel molecular basis for chamber-specific programming of cellular proliferation and maturation in neonatal heart, including potential splicing regulation of dynamic exon enrichment of cell cycle related genes. Further functional studies to decipher putative splicing regulators of CC programming in LV vs. RV during maturation will likely lead to novel chamber-specific regenerative and therapeutic targets.