BME Graduate Student Seminar: Julien Morival

Seminar via Zoom link: https://uci.zoom.us/j/94868015209

Elucidating the role of DNA methylation in cell fate and disease through stem cell models

Abstract: Human pluripotent stem cells (hPSCs) can give rise to almost all the specialized cells that make up the human body. This ability has made PSCs particularly attractive in the search to understand the mechanisms that drive development. Molecular heterogeneity is emerging as a critical feature of multicellular life. While single-cell analyses have revealed the existence of cell-to-cell variation in the levels and activities of the molecules responsible for gene regulation, the source of such variation is still poorly understood. Cytosine methylation is a highly conserved epigenetic modification that plays an important role in mammalian development, and its occurrence within phenotypically uniform cell populations is often variable even at the same genomic location. We recently developed a new sequencing method (Repli-BS) that enables analysis of methylation heterogeneity across cytosine residues within newly replicated strands of DNA over time. Using this method, we discovered that much of the methylation heterogeneity observed within HUES64 human embryonic stem cells (hESCs) is temporal in nature and associated with DNA replication. Using this data set and rates of remethylation generated in collaboration with the Read Lab, we observe that unique patterns of methylome replication associate with distal regulatory regions throughout the genome, enrich for cytosine residues dynamically methylated between stem cells and germ layers, and coincide with the location of stem cell-specific transcription factor binding and chromatin architectures. Simultaneously, we also see that the dynamic behavior of methylation may be itself responsible for the age-associated loss in methylation. Furthermore, induce pluripotent stem cells (iPSCs) are ideal for creating disease models, using skin biopsies from diseased patients. In collaboration with the Zaragoza lab, we performed RRBS on fibroblast and iPSCs acquired from patients exhibiting dilated cardiomyopathy (DCM) in two families with different forms of LMNA mutations. By comparing their DNA methylation profile to those of their non-diseased siblings, we were able to identify differentially methylated regions (DMRs) unique to each family, as well as those shared across the two groups. Interestingly, we observed that although all three categories of DMRs associated with regulatory features and chromatin, only family-specific DMRs associated with unique genes that recapitulated their respective family’s disease phenotypes in fibroblasts. In iPSCs, however, only one of the families seemed to have differential methylation associated with its disease phenotype in this early developmental state. Together, these models provide us with a better understanding of DNA methylation’s function in cell fate and disease. Future work will now focus on trying to design more appropriate and effective epigenetic modifiers that could one day be integrated into these previously stated systems.