Decoding epigenetic adapters of cell state - PROJECT SUMMARY/ABSTRACT Pluripotency is a fleeting state in the embryo that is the source for all the cell types of the body. This enormous developmental potential is facilitated by a permissive genome structure globally depleted for the nucleosomal compaction and heterochromatin that direct lineage acquisition. Amazingly, embryonic stem cells (ESCs) derived from the inner cell mass capture the pluripotent state and its specialized chromatin signature in vitro. As expected, ESCs are enriched for activating histone lysine acetylations, but surprisingly are the most depleted for modifications associated with ongoing transcription found at gene bodies. The epigenome is causal in developmental potential as maintenance of pluripotency-associated modifications inhibits their differentiation and removal of somatic-associated modifications enhances reprogramming to induced pluripotent stem cells (iPSCs). Therefore, dynamic cell state transitions are a powerful platform that will be used mechanistically interrogate the epigenetic contribution to cellular identity. In both the embryo and in ESCs, the global depletion of heterochromatin permits widespread amplification of transcription, despite the near absence of transcription-associated gene body epigenetic modifications. The relative increase in transcriptional output was recently observed in adult stem cells and cancer stem cells, but the connection of developmental potential and the calibration of RNA output is currently unknown. The goal of this research program is to parse the interconnected network of cellular identity, the epigenome, and the global transcriptome. To identify how transcription is amplified, we will examine the regulation of RNA polymerase II checkpoints across cell states. We will define how gene body modifications that enforce the somatic fate regulate transcriptional output using specialized genetic depletion and targeting tools. We will uncover how ESCs interpret their uniquely high levels of histone acetylation to sustain pluripotency. Using acute degradation technologies, we will interrogate how acetylation directs RNA polymerase II across early developmental stages when transcription commences. The findings of our proposed studies extend to regenerative medicine and cancer biology as transcriptional output is a scalable feature of developmental potential across tissue type and cellular identity.
