Gene regulation and the physical genome

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Interpreting genetic or genomic data requires an understanding of DNA as a tangible, dynamic object with particular physical properties. In most eukaryotes, DNA is packaged in the nucleus as chromatin, with proteins called nucleosomes that determine the accessibility of the genome to biochemical activity. In this work, I chart chromatin accessibility and gene expression in a three-dimensional induced stem cell-derived organoid model of human cortical development, nominating specific molecular factors that may drive differentiation and maturation of glial, excitatory neuronal, and inhibitory cell lineages. I identify putative enhancers that may regulate corticogenesis and developmental states that harbor increased vulnerability to genetic perturbations associated with neurodevelopmental disease. Separately, I studied the three-dimensional organization of a unique eukaryotic organism that does not package DNA with nucleosomes, the dinoflagellate Symbiodinium minutum. I found that the domain-scale architecture of its chromosomes was completely dependent on ongoing active transcription, highlighting a fundamental connection between gene expression and genome organization.


Type of resource text
Form electronic resource; remote; computer; online resource
Extent 1 online resource.
Place California
Place [Stanford, California]
Publisher [Stanford University]
Copyright date 2020; ©2020
Publication date 2020; 2020
Issuance monographic
Language English


Author Trevino, Alexandro E
Degree supervisor Greenleaf, William James
Thesis advisor Greenleaf, William James
Thesis advisor Bintu, Lacramioara
Thesis advisor Bryant, Zev David
Thesis advisor Chang, Howard Y. (Howard Yuan-Hao), 1972-
Degree committee member Bintu, Lacramioara
Degree committee member Bryant, Zev David
Degree committee member Chang, Howard Y. (Howard Yuan-Hao), 1972-
Associated with Stanford University, Department of Bioengineering


Genre Theses
Genre Text

Bibliographic information

Statement of responsibility Alexandro Eugene Trevino.
Note Submitted to the Department of Bioengineering.
Thesis Thesis Ph.D. Stanford University 2020.
Location electronic resource

Access conditions

© 2020 by Alexandro E Trevino
This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

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