Characterization of the roles of bivalent domains in CD4+ T cell differentiation - Project Summary/Abstract This K22 proposal describes my plan to obtain the necessary biological and educational skills, which provide me the foundation of developing my independent laboratory. Bivalent domains, which are chromatin regions where H3K4me3 and H3K27me3 coexist, are critical for cellular plasticity. I joined Dr. Zhao lab in order to pursue single cell epigenetic assays. In my postdoc training, I received very diverse and deep trainings, which have broadened my view of immunology, specifically T cell differentiation. Under the guidance of Dr. Zhao, I developed a new assay for profiling histone marks at the single cell level, but its low cell throughput limits its application to complex biological systems. Recently, I have developed a novel technique called iscChIC-seq which enhances the cell throughput. During the mentored phase of this award, I intend to expand my biological skills and apply iscChiC-seq to human CD4+ T cells. To this end, I have asked my biologist colleague to teach me certain experiments. I have asked Dr. Zhao to provide me with proper material, equipment and trainings to perform experiments. Under the guidance of Dr. Zhao and the resources from NHLBI will promote to support my work. Obtaining the necessary biological skills will enable me to setup my research lab and to effectively mentor students and postdoctoral from both computational and biological sciences. The goal of this proposal is to understand the roles of bivalent domains in cellular plasticity during human CD4+ T cell differentiation. In my preliminary analysis, I discovered that T cell plasticity-related genes can be identified using the scRNA-seq data in T cells. I hypothesize that some bivalent domains can regulate these plasticity-related genes. These domains termed as plasticity-related bivalent domains can be identified by histone mark dynamics along the CD4+ T cell differentiation process (Aim1). Previous studies have shown that chromatin re-organization occurs at bivalent domains during T cell differentiation. My preliminary results are consistent with this observation and further support that the chromatin re-organization is a complex dynamic process that has not been described before. Supported by the preliminary results, I propose that the chromatin structure associated with plasticity-related bivalent domains changes from condensed to open during T cell differentiation when new chromatin interactions can be formed and the connection with enhancers can be established. This hypothesis will be examined (Aim2). Finally, I will use the Ezh2 inhibitor to suppress the repressive histone marks (H3K27me3) at bivalent domains during T cell differentiation. Thus, the hypothesis of whether plasticity-related bivalent domains regulate target genes can be validated (Aim 3). These knowledges will be critical in identifying novel targets for drug and vaccine development for immune associated diseases. To ensure the successful completion of this proposal, I have assembled a committee of experts and collaborators that will help me on various aspects of this proposal.
