Innovations in Spatial Nucleomics: Multiplexed Epigenomic Profiling and Next-Generation Tools for FISH Research

Date of Award

Spring 1-1-2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Genetics

First Advisor

Wang, Siyuan

Abstract

Fluorescence in situ hybridization (FISH) technologies have transformed our understanding of the spatial nucleome. These methods offer a unique blend of advantages that make then attractive choices for researchers in both fundamental and clinical studies. Because FISH is non-destructive, its derivative methods may be multiplexed with other imaging modalities for simultaneous visualization of a wide array of cellular morphologies and phenotypes in the same single cells, while preserving the larger context of a tissue environment. In this dissertation, I describe my work to advance the field of spatial omics by developing the first epigenetics profiling method that 1) is non-disruptive to nuclear architecture, and is compatible with chromatin tracing, 2) can profile pairs of epigenetic marks simultaneously across hundreds of genomic targets in the same single cells, and 3) can achieve high genomic resolution, making it suitable for profiling the epigenetic states of small genomic elements such as promoters and enhancers. In addition, I present my work to construct supporting tools for the spatial omics field more broadly, consisting of 1) the first rapid, lightweight, deterministic algorithm for assignment of barcodes to genomic targets in combinatorial FISH, which may be used to significantly reduce experiment cost, and 2) an updated version of our FISH library design software, now called ProbeDealerV2, which has expanded support for cutting-edge FISH methods and includes a complete suite of tools to assist every stage of the design process, all through a revamped user interface. Together, the epigenetics profiling method and supporting tools presented here will contribute to our understanding of the spatial nucleome, while also spurring on the development of the field.

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