Epigenetic mechanisms are crucial for regulating gene expression in development and cell differentiation. Dysregulation of epigenetic information is implicated in many human diseases including cancer. We are interested in understanding how multiple levels of epigenetic mechanisms are regulated in normal development and disease states. By focusing on H1 linker histones, the major chromatin structural proteins facilitating the folding of higher order chromatin structures, we investigate the role of chromatin compaction in development, stem cell biology, and tumorigenesis. We have established H1 and its multiple variants as important epigenetic factors regulating gene expression for development, stem cell differentiation and tumor suppression. We spearheaded genome-wide mapping of H1 variants in embryonic stem cells and further classified H1s as causal repressive marks for silencing satellite repetitive sequences and regulating chromocenter clustering. Using molecular, cellular, genetic and bioinformatic approaches combined with stem cell technologies, we seek to elucidate how epigenetic regulation interplays with signaling pathways in cell fate determination and ultimately to discover novel therapeutic strategies and targets for regenerative medicine and cancer treatment.