Dynamic Changes in DNA Replication Timing and 3D Genome Organization During Cardiac Differentiation

Abstract

Genome architecture has emerged as a key factor of gene regulation and is tightly coordinated with the temporal order of DNA replication (Replication Timing – RT). RT and 3D genome organization change dynamically throughout development in correlation with the establishment of cell type specific gene expression patterns. The first organ to develop during embryonic development is the heart. The heart is a post-mitotic, terminally differentiated organ which, compared to other organs such as the liver, lacks the capacity to regenerate upon injury such as myocardial infarction. Instead, it forms fibrotic tissue that maintains organ integrity but undermines pump function, often leading to congestive heart failure and premature death. Deciphering the 3D genome organization in cardiac differentiation may help our understanding of gene regulation during cardiac development. DNA replication timing (RT) is a very informative functional readout of large-scale chromatin organization across distinct cell types and its regulation during development. RT is cell type-specific, highly conserved and changes in RT affect approximately half the genome during development and differentiation. I hypothesize that changes in the 3D genome organization play a critical role in gene regulation and cell function in cardiac differentiation. In this work, I will differentiate human embryonic stem cells (hESCs) towards cardiomyocytes and use a multiomics approach (RT, transcriptome and 3D genome organization) to identify the dynamic changes in genome architecture, RT and gene expression during normal cardiac development. This will allow us, in the future, to construct an integrative model of nuclear function in cardiac cells that can be leveraged as a framework to identify cellular alterations associated with congenital cardiovascular diseases.