Patty, Benjamin
(2024)
Investigations on the impact of chromatin dynamics on cis-regulatory elements and gene expression in embryonic stem cells.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
This is the latest version of this item.
Abstract
Regulation of gene expression is multifaceted, characterized by a dynamic interplay between numerous proteins and genetic elements. My thesis focuses on understanding how important proteins, termed chromatin remodelers and histone variants, regulate gene expression through interactions with chromatin: the macromolecular structure that compacts and protects DNA. Dynamic restructuring of chromatin by chromatin remodelers and histone variants is critical to proper gene expression, and misregulation of this process in the genetic disorders associated with these factors are abundant. Thus, a fundamental understanding of how these factors regulate chromatin, and what happens to gene expression when they are mutated or lost, is of vital importance to biomedical research.
To understand the role of chromatin remodelers in gene expression, I performed a system-level study to determine how individual loss of the 32 chromatin remodelers found in mouse and human cells alters transcription of three important RNA classes: mRNAs, uaRNAs, and eRNAs. These studies revealed that the regulatory paradigm of remodelers for these three transcript classes is similar in important ways, but also revealed that some remodelers influence these RNA classes in different ways. In follow up studies, I examined how three understudied remodelers (CHD8, SRCAP, and SMARCAL1) regulate chromatin dynamics, describing previously unknown interactions between SRCAP and CHD8 with transcription factors and SMARCAL1 with RNA processing factors that influence transcription. Finally, to further understand the role of histone variant H3.3 in transcriptional regulation in murine embryonic stem cells (mES cells), we attempted to generate H3.3K122A cell lines but were unable to recover cell lines with all four targeted alleles. Through characterization of cell lines with two or three targeted alleles, we find that the H3.3K122A mutation is neomorphic, possibly resulting in cell death by interfering with the functions of H3.3. Thus, H3.3K122 is necessary for viability in mES cells. Together, these studies deepen our understanding of how chromatin remodelers and histone variants perform vital roles in gene expression through regulation of chromatin dynamics.
Share
| Citation/Export: |
|
| Social Networking: |
|
Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
|
| Date: |
27 August 2024 |
| Date Type: |
Publication |
| Defense Date: |
7 May 2024 |
| Approval Date: |
27 August 2024 |
| Submission Date: |
24 June 2024 |
| Access Restriction: |
2 year -- Restrict access to University of Pittsburgh for a period of 2 years. |
| Number of Pages: |
253 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Biological Sciences |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Chromatin, non-coding RNAs, gene regulation, transcription, histone variants, chromatin remodelers, mRNA, chromatin dynamics |
| Date Deposited: |
27 Aug 2024 13:43 |
| Last Modified: |
27 Aug 2024 13:43 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/46645 |
Available Versions of this Item
-
Investigations on the impact of chromatin dynamics on cis-regulatory elements and gene expression in embryonic stem cells. (deposited 27 Aug 2024 13:43)
[Currently Displayed]
Metrics
Monthly Views for the past 3 years
Plum Analytics
Actions (login required)
 |
View Item |
![[img]](http://d-scholarship.pitt.edu/style/images/fileicons/application_pdf.png)
![[feed]](/images/feed-icon-32x32.png){kind=icon}