Epigenetic Reprogramming in Arabidopsis thaliana.
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
Epigenetics regulates a cell's gene expression programme and thus decides its cell type. These epigenetic marks are dynamic during the development of multi-cellular organisms as new cell types are being generated. During regeneration, epigenetic marks must be reset as differentiated somatic cells turn back into stem cells. Plants are especially good at regeneration, and thus we use the model plant Arabidopsis thaliana to study how epigenetic marks are reset.
Specifically, I will study the reprogramming of a developmentally important repressive epigenetic mark, the trimethylation of histone 3 lysine 27 (H3K27Me3). This epigenetic mark regulates over 4000 genes and is highly dynamic and necessary during development. 3 A.thaliana proteins are known that can enzymatically remove this mark and do so at different points in development to allow the expression of developmentally important genes. These 3 "H3K27Me3 demethylases" target genes in a spatially and temporally specific manner so that developmental genes are only activated in the correct specific cells. How the precise spatio-temporal recruitment of H3K27Me3 demethylases to their target genes is achieved is unknown. Additionally, the relationship between the 3 different H3K27Me3 demethylases remains to be resolved. We have observed that H3K27Me3 demethylases are important for proper regeneration, but many questions remain regarding the demethylase's mechanism of action and whether other mechanisms of H3K27Me3 removal contribute to epigenetic reprogramming during regeneration.
Through this PhD project I will apply traditional molecular biology and plant science techniques alongside modern computational biology methods to answer these questions. Our results will provide insight into this unique molecular event in development and reveal how plants generate stem cells from differentiated tissues. Commercially relevant knowledge will also be generated as the 3 H3K27Me3 demethylases are known to regulate important crop traits such as seed development, self-fertilisation and germination rate.
Specifically, I will study the reprogramming of a developmentally important repressive epigenetic mark, the trimethylation of histone 3 lysine 27 (H3K27Me3). This epigenetic mark regulates over 4000 genes and is highly dynamic and necessary during development. 3 A.thaliana proteins are known that can enzymatically remove this mark and do so at different points in development to allow the expression of developmentally important genes. These 3 "H3K27Me3 demethylases" target genes in a spatially and temporally specific manner so that developmental genes are only activated in the correct specific cells. How the precise spatio-temporal recruitment of H3K27Me3 demethylases to their target genes is achieved is unknown. Additionally, the relationship between the 3 different H3K27Me3 demethylases remains to be resolved. We have observed that H3K27Me3 demethylases are important for proper regeneration, but many questions remain regarding the demethylase's mechanism of action and whether other mechanisms of H3K27Me3 removal contribute to epigenetic reprogramming during regeneration.
Through this PhD project I will apply traditional molecular biology and plant science techniques alongside modern computational biology methods to answer these questions. Our results will provide insight into this unique molecular event in development and reveal how plants generate stem cells from differentiated tissues. Commercially relevant knowledge will also be generated as the 3 H3K27Me3 demethylases are known to regulate important crop traits such as seed development, self-fertilisation and germination rate.
Organisations
People |
ORCID iD |
| Jie Song (Primary Supervisor) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011178/1 | 01/10/2015 | 25/02/2025 | |||
| 2133365 | Studentship | BB/M011178/1 | 29/09/2018 | 22/12/2022 |
| Description | We discovered novel functions for 2 epigenetic eraser enzymes in Arabidopsis flower development. Though both epigenetic regulators remove the same histone modification, we discovered that they have antagonistic functions at the developmental level: one affects floral development to promote self-fertilisation whilst the other has the opposite effect to promote out-crossing! This surprising finding prompted us to create a bioinformatic pipeline utilising RNAseq and histone ChIPseq data to predict the target genes of the epigenetic erasers which are responsible for these developmental functions. |
| Exploitation Route | Our work identified roles of epigenetic regulatory enzymes that are of commercial interest; the control of plant self-fertility. Crop sciences companies may be interested in controlling this trait and we have demonstrated that this can be done by mutating key epigenetic regulatory enzymes. |
| Sectors | Agriculture, Food and Drink,Environment |
| URL | https://www.frontiersin.org/articles/10.3389/fpls.2021.640135/full |