Hall Hickman, Alexander;
(2025)
The effects of G-tract RNA on chromatin regulatory proteins.
Doctoral thesis (Ph.D), UCL (University College London).
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Abstract
Nascent RNA has been shown to alter chromatin structure, suggesting that it feeds back information on gene activity to epigenetic state. A number of chromatin regulatory proteins have been found to interact with RNA, including polycomb repressive complex 2 (PRC2), which is essential for development and often mutated in cancer. PRC2 and several other chromatin regulatory proteins preferentially interact with G-quadruplex (G4)-forming G-tract RNA sequences, suggesting that this may represent a particularly active chromatin regulatory RNA element. In this thesis, I test the effect of G-tract RNA on chromatin regulatory proteins, including PRC2. Our laboratory has shown that G-tract elements within nascent pre-mRNAs prevent PRC2 from interacting with chromatin, thus preserving an active chromatin state. Other laboratories contend that RNA recruits PRC2 to chromatin. Thus, the effect of RNA on PRC2 chromatin occupancy and on chromatin states more broadly remains unclear. To explore this, I test the validity of the model that RNA recruits PRC2 to chromatin. I demonstrate that results interpreted by others as RNA-dependent PRC2 chromatin binding are actually due to an experimental artifact that causes nonspecific chromatin precipitation. I find instead that G-tract RNA inhibits the interaction of PRC2 and other chromatin regulators with nucleosomes. Furthermore, by coupling dCas9-mediated RNA tethering with mass spectrometry, I have established a method for determining the broader effect of G-tract RNA on chromatin. I present results validating this approach using immunofluorescence, ChIP-qPCR and preliminary proteomics. These approaches will allow us to understand the effects of RNA on PRC2 recruitment and determine the broader effect of G-tract RNA elements on local chromatin environments.
| Type: | Thesis (Doctoral) |
|---|---|
| Qualification: | Ph.D |
| Title: | The effects of G-tract RNA on chromatin regulatory proteins |
| Language: | English |
| Additional information: | Copyright © The Author 2025. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10204605 |
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