Dissecting Multiscale Interplay between Chromatin Organization and Gene Expression

Abstract

Chromosomes in eukaryote nuclei of cells store genetic information. How chromosomes are organized and how does chromatin organization regulate cellular functions especially transcription has been a long-standing question in cell biology. The development of biochemical and imaging technologies has unveiled distinct chromatin higher-order structures including promoter-enhancer loops, topologically associated domains (TADs), A and B compartments. However, how do these structures manifest in single cells, and how does the 3-dimentional (3D) organization of these structures contribute to functional regulation were not elucidated when my thesis research was started. In this dissertation, I present my development of an imaging-based multimodal omics method and its applications to characterize these structures together with transcriptional states in cultured cell and tissue contexts. In Chapter 1, I reviewed the history of chromatin structures studies and development of technologies to enable these discoveries, in particular, Chromosomal Conformation Capture (3C) based sequencing methods and fluorescence in situ hybridization for DNA (DNA-FISH). In Chapter 2, my colleagues and I developed a multimodal multiplexed error-robust fluorescent in situ hybridization for DNA and RNA (multimodal DNA- and RNA-MERFISH) method to systematically investigate the 3D chromatin organization, nascent transcriptional activity, and nuclear structural protein distribution in single cells. Using this approach, we characterize chromatin domains, compartments, and trans-chromosomal interactions and their relationship to transcription in single cells. In Chapter 3, my colleague and I combined the RNA-MERFISH and DNA-MERFISH to visualize transcriptional states and chromatin organization respectively in the context of mouse primary motor cortex (MOp). We identified cell-type dependent chromatin structures and characterized their relationship with cell type specific transcription. In Chapter 4, I further discussed the technological development and biological application perspectives based on genome-scale chromatin imaging and multimodal imaging.