Methylation-based methods for studying chromatin structure

DNA is decorated with chemical marks and proteins that allow our genome to encode countless distinct cellular states. Proteins in the nucleus interact with DNA and mediate methylation of cytosine bases, modifications to the histones around which DNA wraps, the degree of compaction of DNA, and the spatial localization of DNA within the nucleus. These epigenetic regulatory elements determine the binding of transcriptional machinery that control gene expression and give rise to cellular diversity. Measuring where proteins bind to the genome and how the epigenome regulates gene expression can reveal underlying mechanisms that control cell state and can help uncover how these mechanisms are modified in diseased states. In this dissertation, I describe a suite of tools that measure protein-DNA interactions by encoding these epigenetic features in exogenous methylation of genomic DNA and detecting these marks with DNA sequencing platforms.First, I extend and optimize short-read sequencing techniques for measuring protein-DNA interactions with the goal of applying these methods to single cells. Single-cell measurements capture dynamics occurring in small populations of cells and can reveal coordinated features within a cell that cannot be measured with bulk methods. Short-read methods map features of chromatin structure through base conversion, fragmentation, or selective enrichment of short sequences of DNA and leverage high-throughput DNA sequencing to detect enrichment of these features genome-wide. Next, I detail a method that I developed collaboratively that leverages long-read sequencing to measure protein binding events. Long-read sequencing provides a new dimension in which to encode information about the chromatin structure of a cell because long-read sequencers can read out not only nucleotide bases, but also modifications to those bases. With this new encoding space, we take multi-omic measurements of endogenous DNA methylation directly together with other elements of chromatin structure (e.g., histone modifications, DNA accessibility, DNA spatial localization, and protein binding events) by encoding these elements as DNA base modifications