UC Irvine

DNA replication is of paramount importance in cell proliferation, the process by which cells grow and divide to produce new cells. During this critical phase of the cell cycle, a cell duplicates its DNA, ensuring that each daughter cell receives a complete set of genetic information. Beyond mere duplication of genetic material, DNA replication also involves the crucial task of recovering the epigenome. The epigenome plays a fundamental role in regulating gene expression without changing the underlying DNA sequence. Epigenetic modifications need to be precisely and efficiently duplicated and transferred onto newly synthesized DNA post-replication, allowing the preservation of cellular identity and function across generations. It is within this context that cell fate transitions may occur. As the cell duplicates its genome and epigenome, modifications can be introduced or removed, and chromatin architecture can change, leading to alteration in gene expression that could potentially trigger a cell to leave its original state and transition into a different cell type. Therefore, DNA replication represents a critical window for the study of cell fate decisions in human embryonic stem cells and offers unique insights into the dynamic nature of the epigenome and its influence on cellular identity and development.Due to the underexplored nature of this phase of the cell cycle, we lack the technologies to be able to reliably assay changes during and post-DNA replication. In this work, technologies were developed to provide a means to this end. First, Repli-ATAC-seq was developed to understand how the chromatin landscape is reestablished in post-replication time by assaying chromatin accessibility. This assay shed light on nucleosome dynamics after replication, bringing to light the potential timing of accessibility changes that may be reflected in biological processes such as DNA mismatch repair, transcription factor accessibility binding dynamics, and an association between increased accessibility and high gene expression. Furthermore, an S-phase fractioned single cell 10X Multiome ATAC and Gene Expression assay was produced to understand if and how chromatin architecture and gene expression are related during S-phase, and whether or not there are clues to explore cell state identities throughout S-phase. Remarkably, a neuroectodermal contributor DACH1 revealed itself as a contributor to a potentially primed cell identity in S-phase. This work establishes techniques that could be used to identify cell cycle dynamics of chromatin accessibility and associated biological changes.