COMPASS-mediated Transgenerational Epigenetic Inheritance in Caenorhabditis elegans
Lead Research Organisation:
University of Leeds
Department Name: Inst of Molecular & Cellular Biology
Abstract
COMPASS is a conserved eukaryotic histone methyltransferase complex, responsible for the trimethylation of lysine 4 on the N-terminal tail of histone 3. This modification, abbreviated H3K4me3, is a hallmark of active promoters.
This project seeks to explore the role of COMPASS in transgenerational epigenetic inheritance, which is the inheritance of traits between multiple generations independently of the genetic code. This phenomenon was first reported in C. elegans in 2011, when genetically wild-type descendants of various mutants of the COMPASS complex subunits were demonstrated to inherit the long-lived phenotype of their allelic mutant ancestor for four generations (Greer et al. 2011).
Studies comparing histone modification levels between different conditions in C. elegans typically rely on antibody-based techniques such as immunofluorescence, which are only semi-quantitative, depending on the performance and specificity of the antibody. This project will establish a purely quantitative liquid-chromatography-coupled tandem mass spectrometry (LC-MS/MS) pipeline for C. elegans -derived histones, in collaboration with the Dickman group at the University of Sheffield, who have expertise in histone proteomics.
The project will begin with a pilot study comparing the histone modification landscape in two loss-of-function COMPASS mutants, set-2(bn129) and cfp-1(tm6369) with wild-type (N2). Once the method is established, the LC-MS/MS pipeline will be used to address two transgenerational epigenetic inheritance questions. The first concerns the transgenerational temperature-sensitive sterility observed in set-2(bn129) mutants (Robert et al. 2014). It will be informative to use the LC-MS/MS approach to assess whether there is a change in the histone modification landscape between different generations of the set-2(bn129) and cfp-1(tm6369) mutants. The second question concerns the changes in the histone modification landscape during the recovery of wild-type descendants in the generations post-crossing of a set-2(bn129) hermaphrodite into the wild-type (N2) background.
Phenotypic assays assessing brood size, lifespan and developmental rate of descendants will shed further light on the phenotypic consequences of descending from a COMPASS loss-of-function background. Immunofluorescence of C. elegans germlines using antibodies against selected histone post-translation modifications (PTMs) of interest will confirm any interesting hits from the LC-MS/MS analysis.
Greer, E. L., T. J. Maures, D. Ucar, A. G. Hauswirth, E. Mancini, J. P. Lim, B. A. Benayoun, Y. Shi & A. Brunet (2011) Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature, 479, 365-U204.
Robert, V. J., M. G. Mercier, C. Bedet, S. Janczarski, J. Merlet, S. Garvis, R. Ciosk & F. Palladino (2014) The SET-2/SET1 Histone H3K4 Methyltransferase Maintains Pluripotency in the Caenorhabditis elegans Germline. Cell Reports, 9, 443-450.
This project seeks to explore the role of COMPASS in transgenerational epigenetic inheritance, which is the inheritance of traits between multiple generations independently of the genetic code. This phenomenon was first reported in C. elegans in 2011, when genetically wild-type descendants of various mutants of the COMPASS complex subunits were demonstrated to inherit the long-lived phenotype of their allelic mutant ancestor for four generations (Greer et al. 2011).
Studies comparing histone modification levels between different conditions in C. elegans typically rely on antibody-based techniques such as immunofluorescence, which are only semi-quantitative, depending on the performance and specificity of the antibody. This project will establish a purely quantitative liquid-chromatography-coupled tandem mass spectrometry (LC-MS/MS) pipeline for C. elegans -derived histones, in collaboration with the Dickman group at the University of Sheffield, who have expertise in histone proteomics.
The project will begin with a pilot study comparing the histone modification landscape in two loss-of-function COMPASS mutants, set-2(bn129) and cfp-1(tm6369) with wild-type (N2). Once the method is established, the LC-MS/MS pipeline will be used to address two transgenerational epigenetic inheritance questions. The first concerns the transgenerational temperature-sensitive sterility observed in set-2(bn129) mutants (Robert et al. 2014). It will be informative to use the LC-MS/MS approach to assess whether there is a change in the histone modification landscape between different generations of the set-2(bn129) and cfp-1(tm6369) mutants. The second question concerns the changes in the histone modification landscape during the recovery of wild-type descendants in the generations post-crossing of a set-2(bn129) hermaphrodite into the wild-type (N2) background.
Phenotypic assays assessing brood size, lifespan and developmental rate of descendants will shed further light on the phenotypic consequences of descending from a COMPASS loss-of-function background. Immunofluorescence of C. elegans germlines using antibodies against selected histone post-translation modifications (PTMs) of interest will confirm any interesting hits from the LC-MS/MS analysis.
Greer, E. L., T. J. Maures, D. Ucar, A. G. Hauswirth, E. Mancini, J. P. Lim, B. A. Benayoun, Y. Shi & A. Brunet (2011) Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature, 479, 365-U204.
Robert, V. J., M. G. Mercier, C. Bedet, S. Janczarski, J. Merlet, S. Garvis, R. Ciosk & F. Palladino (2014) The SET-2/SET1 Histone H3K4 Methyltransferase Maintains Pluripotency in the Caenorhabditis elegans Germline. Cell Reports, 9, 443-450.
People |
ORCID iD |
| Ian Hope (Primary Supervisor) | |
| Rosamund Clifford (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| MR/N013840/1 | 01/10/2016 | 30/09/2025 | |||
| 1789839 | Studentship | MR/N013840/1 | 01/10/2016 | 31/08/2020 | Rosamund Clifford |
| Description | Genetics Society Junior Scientist Conference Grant |
| Amount | £750 (GBP) |
| Organisation | The Genetics Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 06/2019 |
| Description | Genetics Society own meeting Junior Scientist Travel Award |
| Amount | £200 (GBP) |
| Organisation | The Genetics Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 04/2017 |
| Description | MRC Flexible Fund |
| Amount | £6,656 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 09/2019 |
| Description | Liquid chromatography coupled tandem mass spectrometry based analysis of histone post-translational modifications in C. elegans |
| Organisation | University of Sheffield |
| Department | Department of Chemical and Biological Engineering |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I have purified histone extracts from C. elegans embryos and germlines, and provided these samples to the collaborator for analysis. I have visited the lab in Sheffield on many occasions and learned to prepare the histones for LC-MS/MS (by proprionylation and trypsin digestion) and thus gained experience of new lab techniques. More recently I have also been learning how to perform the downstream analysis of the LC-MS/MS results using Epiprofile and Skyline software. I been to lab meetings with the Sheffield group and presented at one myself. |
| Collaborator Contribution | The collaborators in Sheffield have shared their expertise in all aspects of histone proteomics. Their help has been invaluable in completing the majority of my PhD research. They have taught me new lab techniques and data analysis methods. |
| Impact | Data generated from this collaboration is as yet unpublished, but I anticipate it will be soon. The experience I have gained from the collaboration enabled me to secure a placement for summer 2019 working on mass spectrometry imaging. |
| Start Year | 2016 |
| Description | International C. elegans meeting 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the largest international C. elegans conference. I spoke to researchers at PI, post-doc and PhD level from multiple institutions all over the world. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Leeds Omics Research in Progress talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | The Leeds Omics Researchers in Progress talks have just been started this year and are intended to provide an opportunity for postgraduate researchers to describe their research, in any of the 'omics' areas, to a mixed audience of predominantly PhD students, but also post-docs and PIs. About 30 researchers attended my talk, and there was an in depth discussion of the results and methodology afterwards which resulted in me receiving some helpful advice and a protocol for a complementary set of experiments to the ones I am doing. |
| Year(s) Of Engagement Activity | 2019 |
| Description | University of Leeds Faculty of Biological Sciences Postgraduate Research Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | The symposium takes place every year, and engages the whole Faculty of Biological Sciences. In my first year (2017) I presented a flash talk on my PhD research, and the next year (2018) I presented a poster. This year I will be giving a 20 minute talk. |
| Year(s) Of Engagement Activity | 2017,2018,2019 |