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Development of Single-Cell SPRITE: A Tool for Measuring Heterogeneity of 3D DNA Organization

Citation

Arrastia, Mary Villanueva (2022) Development of Single-Cell SPRITE: A Tool for Measuring Heterogeneity of 3D DNA Organization. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/w70x-2294. https://resolver.caltech.edu/CaltechTHESIS:10012021-223453672

Abstract

Across eukaryotic cells, DNA from each nucleus is organized in three dimensions in order to help regulate transcriptional activity. Decades of chromosome capture technologies have revealed fundamental chromatin structures, providing information about how DNA is assembled genome-wide. The majority of these methods utilize direct physical ligation of DNA molecules to generate pairwise interactions, which have provided information about short-range interactions and intra-chromosomal structures. Recent technologies have moved toward identifying multiple DNA interactions simultaneously without physical ligation of DNA molecules, revealing information about long-range interactions and inter-chromosomal structures. One of the biggest limitations of these methods is that they only study DNA organization in bulk, which misses the heterogeneity of chromosomal structures at the single-cell level. As a result, single-cell chromosome capture methods have been developed to begin probing into the cell-to-cell variability of DNA organization and answer long-standing questions regarding single-cell structure. However, single-cell methods are currently limited to identifying low-resolution, intra-chromosomal DNA interactions with few numbers of cells. This creates a need for an improved, high-throughput single-cell method that can capture high-resolution structures and simultaneous mapping of both intra- and inter-chromosomal interactions to better elucidate single-cell DNA organization. In this thesis, we describe the development of 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE), a single-cell chromosome capture method that allows for mapping of high-resolution, intra- and inter-chromosomal structures across thousands of cells. Through scSPRITE, we were not only able to reveal fundamental information about single-cell DNA organizations, but we can also quantitatively measure the variability of DNA interactions from cell to cell.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:single cell; DNA organization; genomics; nuclear bodies; 3D genome
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Awards:Herbert Newby McCoy Award, 2021
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Ismagilov, Rustem F.
Thesis Committee:
  • Dougherty, Dennis A. (chair)
  • Cai, Long
  • Guttman, Mitchell
  • Ismagilov, Rustem F.
Defense Date:27 September 2021
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
Earle C. Anthony Graduate FellowshipUNSPECIFIED
Record Number:CaltechTHESIS:10012021-223453672
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:10012021-223453672
DOI:10.7907/w70x-2294
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41587-021-00998-1DOIArticle adapted for Chapter 2.
ORCID:
AuthorORCID
Arrastia, Mary Villanueva0000-0002-0723-3574
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14382
Collection:CaltechTHESIS
Deposited By: Mary Arrastia
Deposited On:14 Oct 2021 19:29
Last Modified:21 Oct 2021 19:06

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