Date of Award

Fall 2021

Project Type


Program or Major


Degree Name

Master of Science

First Advisor

Feixia FC Chu

Second Advisor

Xuanmao XC Chen

Third Advisor

Kyung Jae KJJ Jeong


Heart disease is the leading cause of death in the United States, constituting a quarter of total deaths every year. One reason behind the high mortality of heart disease is the limited regenerative capacity of cardiomyocytes (CMs), which carry out the contractile function for the heart. Lineage-specific differentiation of pluripotent stem cells into CMs provides a promising therapeutic strategy, warranting in-depth research for the mechanistic understanding of this sophisticated process to achieve homogenous production of cardiomyocytes with high purity and large quantity. Three-dimensional culture systems, such as microporous hydrogel, have been demonstrated to promote CM differentiation but little is known about the underlying mechanism. This project focuses on histone proteins, which are important components of nucleosome, and their modifications regulate a multitude of cellular processes include differentiation. Using quantitative mass spectrometric analysis, changes in histone modification landscape during embryonic stem cell (ESC) differentiation were characterized and a substantial upregulation in histone H4 Lys16 acetylation (H4 K16ac) was detected in cells enriched in cardiomyocytes. Interestingly, H4 K16ac was also significantly increased in cells cultured in hydrogels, suggesting that hydrogel culture potentially primes the epigenetic state of ESCs for cardiomyocyte differentiation. To better understand signaling pathways involved in mechanosensing of hydrogel environment, we quantitatively compared the Phosphoproteomics of ESCs cultured in hydrogel 3D environment and on 2D tissue culture plates. Together, our results provide novel molecular insights on how mechanosensing signaling regulates epigenome transformation to promote lineage specification.