Exploring Genome Structure During Self-Renewal and the Exit from Pluripotency

This project has two aims. Firstly, I would like to utilize previously calculated 3D genome structures in mouse embryonic stem cells (mESCs) to study structural changes in nuclear architecture. In particular, through the study of large populations of cells, chromatin has been partitioned into two compartments[1], A and B, seen to correspond with regions of transcriptional activity and inactivity respectively. In previous research, considering single mESCs, I extended the notion of chromatin compartments into a continuous metric, insulation. I would like to use this insulation metric to address the following questions. What are the distributions of insulations for highly expressed genes? Do genes move between the A and B compartments when they become activated? How do gene-specific insulation distributions change during differentiation? Are there insulation-associated or conformational entropic changes associated with the early and late stages of differentiation? Secondly, I would like to utilize Bayesian inference techniques to infer higher accuracy nuclear architectures in mESCs. In particular, I will integrate imaging, ChIP-seq and Hi-C contact data to estimate maximum likelihood parameters previously used in structural calculations by Stevens et al.[2] as well as provide statistically rigorous uncertainty estimates on calculated chromatin conformations. Specifically, I will introduce a local structural parameter to directly model chromatin compaction within individual cell nuclei. To investigate these questions, I will use data generated by previously proposed experimental protocols investigating the function of heterochromatin protein 1 (HP1) within the Laue lab.