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Integrated Spatial Genomics Reveals Organizational Principles of Single-Cell Nuclear Architecture


Takei, Yodai (2021) Integrated Spatial Genomics Reveals Organizational Principles of Single-Cell Nuclear Architecture. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/4ces-zm75.


Three-dimensional (3D) nuclear architecture plays key roles in many cellular processes such as gene regulation and genome replication. Recent sequencing-based and imaging-based single-cell studies have characterized a high variability of nuclear features in individual cells from a wide-range of measurement modalities, such as chromosome structures, subnuclear structures, chromatin states, and nascent transcription. However, the lack of technologies that allow us to interrelate those nuclear features simultaneously in the same single cells limits our understanding of nuclear architecture. To overcome this limitation, a technology that can examine 3D nuclear features across modalities from the same single cells is required. Here, we demonstrate integrated spatial genomics approaches, which enable genome-wide investigation of chromosome structures, subnuclear structures, chromatin states, and transcriptional states in individual cells. In Chapter 2, we introduce the "track first and identify later" approach, which enables multiplexed tracking of genomic loci in live cells by combining CRISPR/Cas9 live imaging and DNA sequential fluorescence in situ hybridization (DNA seqFISH) technologies. We demonstrate our approach by resolving the dynamics of 12 unique subtelomeric loci in mouse embryonic stem (ES) cells. In Chapter 3, we present the intron seqFISH technology, which enables transcriptome-scale gene expression profiling at their nascent transcription active sites in individual nuclei in mouse ES cells and fibroblasts, along with mRNA and lncRNA seqFISH and immunofluorescence. We show the transcription active sites position at the surfaces of chromosome territories with variable inter-chromosomal organization in individual nuclei. By building upon those technologies, in Chapter 4, we demonstrate integrated spatial genomics in mouse ES cells, which enables to image thousands of genomic loci by DNA seqFISH+, along with sequential immunofluorescence and RNA seqFISH in individual cells. We show "fixed loci" that are invariably associated with specific subnuclear structures across hundreds of single cells that can constrain nuclear architecture in individual nuclei. In addition, we find individual genomic loci appear to be pre-positioned to specific nuclear compartments with different frequencies, which are independent from nascent transcriptional states of single cells. Lastly, in Chapter 5, we demonstrate the integrated spatial genomics technology in the mouse brain cortex, enabling the investigation of single-cell nuclear architecture in a cell-type specific fashion as well as the exploration of common organizational principles of nuclear architecture across cell types. We reveal that inter-chromosomal organization and radial positioning of chromosomes are arranged with cell-type specific chromatin fixed loci and subnuclear structure organization in diverse cell types. We also uncover the variable organization of chromosome domain structures at the sub-megabase scale in individual cells, which can be obscured with bulk measurements. Together, these results demonstrate the ability of integrated spatial genomics to advance our overall understanding of single-cell nuclear architecture in various biological systems.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Single cell biology; highly multiplexed imaging; spatial (epi)genomics/transcriptomics
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Cai, Long
Thesis Committee:
  • Elowitz, Michael B. (chair)
  • Guttman, Mitchell
  • Rothenberg, Ellen V.
  • Cai, Long
Defense Date:24 May 2021
Record Number:CaltechTHESIS:06022021-012404326
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter 2. adapted for Chapter 3. adapted for Chapter 4. adapted for Chapter 5.
Takei, Yodai0000-0002-7226-5185
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14227
Deposited By: Yodai Takei
Deposited On:03 Jun 2021 00:14
Last Modified:26 Oct 2021 20:49

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