Under pathological stress, an otherwise healthy heart may enter hypertrophy, a partially-reversible, compromised state wherein heart function is relatively normal although the muscle cells increase in size. Should the stress continue, however, the heart will succumb to the irreversible condition of heart failure, resulting in an inability to efficaciously pump enough blood to support bodily demands. When the heart enters states of either hypertrophy or failure, noticeable changes in chromatin accessibility and gene expression arise. Chromatin accessibility can be defined by a binary chromatin state model: heterochromatin is tightly packed and contains silenced genes, while the relatively loose conformation of euchromatin is more conductive to active gene transcription. Alternations in gene expression or epigenetic regulation are revealed using high-throughput sequencing techniques, which have been developed and rigorously applied over the last two decades. How the principles revealed from studies of chromatin impact gene expression levels in the diseased heart is unknown. My dissertation studied the role of multiple chromatin regulator factors, as studied by high-throughput sequencing techniques, contribute to function of the normal and diseased heart. Those factors include a histone modifying enzyme, a nucleosome remodeling protein, circular RNAs and DNA methylation.
The first two chapters of my dissertation detail the functions of two chromatin remodelers identified by quantitative proteomics using mouse hypertrophy and heart failure models: Smyd1, a histone methyltransferase coding gene containing the SET and MYND domains, and Napl14, nucleosome assembly protein 1-like 4. Chapter 1 reports that the chromatin-binding protein Smyd1 restricts adult mammalian heart growth. Mice with induced knockdown of cardiac-specific Smyd1 displayed cardiomyocyte growth, organ remodeling, and declined heart function. Chapter 2 describes a possible mechanism by which histone chaperone Nap1l4 may regulate cardiac transcription in hypertrophy. As revealed by siRNA knock down, the lack of Nap1l4-mediated transcription reduces the size of neonatal rat ventricular myocytes (NRVMs) and inhibits fetal gene reprogramming induced by phenylephrine (PHE). However, when Nap1l4 is overexpressed, there is an increase in the size of NRVMs.
The latter two chapters of the dissertation describe the epigenomic changes revealed by high-throughput sequencing that could potentially affect gene expression during cardiovascular diseases. Chapter 3 explores our utilization of Ribo-Zero RNA sequencing to discover circular RNAs (circRNAs) in the heart using mouse models. We confirmed the existence of cardiac-related circRNAs including circMyocd, circRyr2, and circTtn. With the successful knockdown of circMyocd in NRVMs, we observed increased expression of linear Myocd, indicating the circRNAs may regulate transcription of its linear counterparts. Chapter 4 characterizes DNA methylation alterations in patients undergoing coronary artery bypass grafting (CABG) using reduced representation bisulfite sequencing (RRBS) with respect to post-operative atrial fibrillation (POAF). When comparing pre-operative and post-operative epigenomic states, we found that the hypervariable CpG sites are mostly enriched in or around genes pertaining to the immune system, cellular adhesion and the cardiovascular system. Specifically, altered CpG methylation in genes coding for transforming growth factor-beta 1 (TGF-β1) may be a marker for POAF as well as pre-operative and post-operative epigenomic states. My dissertation revealed that epigenetic changes including chromatin remodelers, DNA methylation and circRNAs could affect the gene expression during heart diseases. The work will undoubtedly benefit the whole community and shed light on the translational medicine for heart failure patients.