RNA-mediated programming of active chromatin
Abstract/Contents
- Abstract
- Various long noncoding RNAs (lncRNAs) have been recently identified, but their functions remain unknown. To better understand the role of lncRNAs in gene activation, we have characterized a 3.76 kilobase highly conserved lncRNA, called HOTTIP, found at the 5' distal tip of the HoxA locus. HOTTIP is required for the expression of HoxA9 to HoxA13 in human fibroblasts and chicken embryos. This region spans a linear 40 kilobases, but forms a compact three dimensional DNA structure by high throughput chromosome conformation capture. Knockdown of HOTTIP causes loss of the activating histone H3K4 trimethylation mark, as well as lost occupancy of the MLL methylase complex by chromatin immunoprecipitation coupled with tiling microarray analysis. To cause these changes, HOTTIP binds WDR5, a component of the MLL complex, to alter histone H3K4 trimethylation and gene activation. Together, the characterization of HOTTIP demonstrates an example of lncRNA-mediated epigenetic activation. A close examination of the binding interaction between HOTTIP and WDR5 has further revealed a novel pathway of lncRNA-regulated proteolysis. HOTTIP acts as a "molecular switch, " causing increased WDR5 protein levels by preventing proteasomal degradation through thermodynamic stabilization post poly-ubiquitination. Increased WDR5 deposition then causes gene activation. One HOTTIP RNA binds a single WDR5 protein through a direct RNA-protein interaction, and RNA-mediated stabilization requires a specific HOTTIP RNA domain in a long RNA context. Using a small scale alanine scanning mutagenesis screen, the HOTTIP binding interface on WDR5 has been identified as the cleft between blades 5 and 6. WDR5 mutations that abrogate lncRNA binding cannot be stabilized by HOTTIP, and are defective in gene activation, maintenance of histone H3K4 trimethylation, and embryonic stem cell self renewal. By altering protein turnover, lncRNAs may be able to regulate the temporal landscape of proteins in cells, potentially altering epigenetic states and cellular functions.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2012 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Yang, Yul Wonjun |
|---|---|
| Associated with | Stanford University, Cancer Biology Program. |
| Primary advisor | Chang, Howard |
| Thesis advisor | Chang, Howard |
| Thesis advisor | Khavari, Paul A |
| Thesis advisor | Kim, Seung K |
| Thesis advisor | Wysocka, Joanna, Ph. D |
| Advisor | Khavari, Paul A |
| Advisor | Kim, Seung K |
| Advisor | Wysocka, Joanna, Ph. D |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Yul Wonjun Yang. |
|---|---|
| Note | Submitted to the Program in Cancer Biology. |
| Thesis | Ph.D. Stanford University 2012 |
| Location | electronic resource |
Access conditions
- Copyright
- © 2012 by Yul Wonjun Yang
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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