Chromatin-mediated regulation of neighboring genes in mammalian synthetic circuits
Abstract/Contents
- Abstract
- In mammalian cells, genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding the dynamics of this transcriptional regulation is important for natural processes, such as heterochromatin spreading during development, aging, and disease, and for designing synthetic gene regulation circuits. In this work, we systematically dissect this spreading behavior in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that with the Kruppel associated box (KRAB), a repressive domain associated with histone methylation, silencing spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by polycomb repressive complex 2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. We find that gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Lastly, our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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 | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Lensch, Sarah |
|---|---|
| Degree supervisor | Bintu, Lacramioara |
| Thesis advisor | Bintu, Lacramioara |
| Thesis advisor | Covert, Markus |
| Thesis advisor | Qi, Lei, (Professor of Bioengineering) |
| Degree committee member | Covert, Markus |
| Degree committee member | Qi, Lei, (Professor of Bioengineering) |
| Associated with | Stanford University, Department of Bioengineering |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Sarah Lensch. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/xf256mv6807 |
Access conditions
- Copyright
- © 2022 by Sarah Lensch
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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