Using chromatin dynamics to understand transcriptional regulation and genetic variance
Abstract/Contents
- Abstract
- The genome is the same in every cell of an organism, but complex organisms have multiple cell types. This is due to the epigenome specifying a cell's transcriptional state resulting in distinct cell identities. Despite 98.5% of the human genome is non-coding and the site of epigenomic activity, which specifies instructions for regulating transcription of the coding region, relatively little is known about its function. A major hurdle with studying non-coding regulatory elements is identifying their distal gene and regulatory targets. Here, I solve this issue by using the three-dimensional chromatin conformation to identify targets that are in close physical proximity of the regulatory element. By integrating data on the three-dimensional chromatin state with other epigenomic measures including the open chromatin regions, transcription factor binding sites, and histone modifications I provide genome-wide insight into how the epigenome establishes the transcriptional state of the cell. In addition, I have developed a new method for prioritizing non-coding genetic variants in complex phenotypes. I validated this method in the context of Type 1 Diabetes and craniofacial disorders. In this dissertation, I demonstrate how data integration of multiple measurements of the epigenome and transcriptome provides insight into methods of transcriptional regulation and how this regulation is influenced by genetic variance.
Description
| 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 |
Creators/Contributors
| Author | Piekos, Samantha Nicole |
|---|---|
| Degree supervisor | Oro, Anthony, 1958- |
| Thesis advisor | Oro, Anthony, 1958- |
| Thesis advisor | Greenleaf, William James |
| Thesis advisor | Wernig, Marius |
| Thesis advisor | Wysocka, Joanna, Ph. D. |
| Degree committee member | Greenleaf, William James |
| Degree committee member | Wernig, Marius |
| Degree committee member | Wysocka, Joanna, Ph. D. |
| Associated with | Stanford University, Department of Stem Cell Biology and Regenerative Medicine |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Samantha Nicole Piekos. |
|---|---|
| Note | Submitted to the Department of Stem Cell Biology and Regenerative Medicine. |
| Thesis | Thesis Ph.D. Stanford University 2020. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2020 by Samantha Nicole Piekos
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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