Role of HP1Beta in chromatin organization during exit from naive pluripotency of mouse embryonic stem cells (mESCs)
Lead Research Organisation:
University of Cambridge
Department Name: Biochemistry
Abstract
Theme: World-Class Underpinning Bioscience
The exit of mESCs from naive pluripotency - a state characterized by the ability of the cells to give rise to any cell type in the embryo - is accompanied by large-scale changes in chromatin structure. My PhD project focusses on the role of heterochromatin protein 1Beta (HP1Beta) in this process. I employ single particle tracking to determine diffusion properties of HP1Beta and the kinetics of its interaction with chromatin, which could help us gain mechanistic insights into heterochromatin dynamics during differentiation.
The exit of mESCs from naive pluripotency - a state characterized by the ability of the cells to give rise to any cell type in the embryo - is accompanied by large-scale changes in chromatin structure. My PhD project focusses on the role of heterochromatin protein 1Beta (HP1Beta) in this process. I employ single particle tracking to determine diffusion properties of HP1Beta and the kinetics of its interaction with chromatin, which could help us gain mechanistic insights into heterochromatin dynamics during differentiation.
| Title | Algorithm for single molecule trajectory analysis |
| Description | This novel method for single-molecule trajectory data analysis relies on calculation of four different parameters describing particle diffusion, and then uses Gaussian mixture modeling to classify the behaviour of particles and detect changes in this behaviour. It has mostly been developed by our collaborators at Ecole Normale Superieure, but with significant input from our side, supported by the BBSRC grant. |
| Type Of Material | Data analysis technique |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | This data analysis technique is used in the lab in several ongoing projects, including one supported by the BBSRC grant, and proves useful in various contexts. |
| Description | Investigating HP1beta dynamics upon differentiation of mES cells with 3D single molecule imaging |
| Organisation | University of Cambridge |
| Department | Department of Chemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Carrying out experimental work: growing and labeling cells, and acquiring microscopy data, using the microscope built by CU Chemistry Dept. Carrying out data analysis, using the new framework provided by ENS IB. |
| Collaborator Contribution | CU Chemistry Dept Building of a novel microscope, capable of single molecule imaging in multiple colours in 3D (using double helix point spread function method) in either live or fixed cells. ENS IB Developing a new method for analysis of single molecule tracking data, using Gaussian mixture model. Help in data interpretation in light of chromatin polymer models. |
| Impact | Outcomes: Poster at the EMBO/EMBL symposium "Seeing is believing" 2019 (see "Engagement activities"). Development of an algorithm for single-molecule trajectory analysis (see "Research databases and models"). Multi-disciplinary: molecular biology, chemistry, engineering, biophysics |
| Start Year | 2014 |
| Description | Investigating HP1beta dynamics upon differentiation of mES cells with 3D single molecule imaging |
| Organisation | École Normale Supérieure, Paris |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Carrying out experimental work: growing and labeling cells, and acquiring microscopy data, using the microscope built by CU Chemistry Dept. Carrying out data analysis, using the new framework provided by ENS IB. |
| Collaborator Contribution | CU Chemistry Dept Building of a novel microscope, capable of single molecule imaging in multiple colours in 3D (using double helix point spread function method) in either live or fixed cells. ENS IB Developing a new method for analysis of single molecule tracking data, using Gaussian mixture model. Help in data interpretation in light of chromatin polymer models. |
| Impact | Outcomes: Poster at the EMBO/EMBL symposium "Seeing is believing" 2019 (see "Engagement activities"). Development of an algorithm for single-molecule trajectory analysis (see "Research databases and models"). Multi-disciplinary: molecular biology, chemistry, engineering, biophysics |
| Start Year | 2014 |
| Description | Investigating the role of HP1beta in chromatin reorganisation upon differentiation of mES cells |
| Organisation | Wellcome Trust |
| Department | Wellcome - MRC Cambridge Stem Cell Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Carrying out experiments, concentrating on studying HP1beta, such as RT-qPCR and ChIP-seq, as well as single molecule imaging. |
| Collaborator Contribution | Expertise in stem cell biology and molecular biology tools used in chromatin biology research, such as RT-qPCR and ChIP-seq. Creating cell lines with protein tags. |
| Impact | Poster at the EMBL/EMBO symposium "Seeing is Believing" 2019 (see "Engagement activities"). |
| Start Year | 2011 |
| Description | Cambridge University Postgraduate Outreach |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Gave two talks/workshops as part of the Cambridge University Postgraduate Outreach Programme. Each was attended by about 10 high school students, who were visiting the University. The pupils were inspired by research in molecular biology in general and in chromatin structure in particular, and a couple of them said that this is likely to influence their choice of the subject they would like to study at the university as well as their future career. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation at EMBO/EMBL symposium "Seeing is Believing - Imaging the Molecular Processes of Life" 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A poster titled "Role of HP1ß in chromatin organization during exit from naive pluripotency of mouse embryonic stem cells (mESCs)" was presented at a major international meeting of the microscopy community. The research presented was discussed with many researchers in the same and neighbouring fields, and sparked a substantial amount of interest. A few ideas for further directions as well as potential collaborations stemmed from this engagement activity. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Resource on Epigenetics for HE+ Pre-16 and Post-16 Educational Websites |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | I developed a resource on Epigenetic for both pre-16 and post-16 branches of the HE+ educational website, targeted at school pupils interested to learn something beyond the scope of the school curriculum, as well as intending to go to a university. The material for the post-16 webpage has been published and so far 91 users found it useful. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.myheplus.com/post-16/subjects/biology/epigenetics |