Reading the Epigenome: Applications and Innovations in Chromatin Profiling

Abstract

The regulation of cell identity is encoded in the chromatin landscape long before transcriptional programs become apparent. However, our ability to interpret and engineer this code has been limited by gaps in mechanistic understanding, a lack of comprehensive reference maps, and the resolution constraints of current technologies. This dissertation establishes a foundational framework for epigenomics across these three dimensions. First, to uncover the mechanistic barriers to cell engineering, we investigate chromatin remodeling during hepatocyte-to-biliary reprogramming. We demonstrate that this lineage conversion is epigenetically incomplete and identify the histone acetyltransferase HBO1 as a critical barrier to plasticity; its depletion enables full lineage conversion. Second, to decode the regulatory logic of lineage specification, we construct a high-resolution CUT&RUN atlas of the mouse immune system. This resource resolves lineage-specific and shared chromatin programs, providing a "regulatory guidebook" for understanding priming, memory, and bivalency across hematopoietic lineages. Third, to bridge the gap between tissue context and chromatin state, we introduce Photoselective Sequencing (PSS), a method that links spatial information to local epigenetic patterns within complex tissues. Finally, to push the limits of resolution, we describe a single-cell profiling approach that combines expansion microscopy with scCUT&Tag to achieve high-resolution mapping of histone modifications alongside cellular morphology. Collectively, these studies illustrate how new experimental and computational strategies are reshaping our understanding of chromatin dynamics, moving the field from static observation toward the rational engineering of cell fate.