Epigenetic regulation of plant reproductive development
Lead Research Organisation:
John Innes Centre
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Employing a combination of molecular, genetic, imaging, epigenetic and genomic approaches, we aim to dissect the mechanisms by which epigenetic factors shape the function and fate determination of the male sexual lineage. Revealing novel genetic and epigenetic regulators and their crosstalk is essential for our knowledge of sexual reproduction, and, at a more fundamental level, important for understanding how the development of a specific lineage of cells is tightly controlled in the context of a plastic environment of plant development.
Planned Impact
unavailable
Organisations
- John Innes Centre (Lead Research Organisation)
- Chinese Academy of Sciences (Collaboration)
- Tokyo Metropolitan University (Collaboration)
- Seoul National University (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- University of Hamburg (Collaboration)
- National Laboratory of Genomics for Biodiversity (Collaboration)
- University of California, Berkeley (Collaboration)
People |
ORCID iD |
| Xiaoqi Feng (Principal Investigator) |
Publications
Buttress T
(2022)
Histone H2B.8 compacts flowering plant sperm through chromatin phase separation.
in Nature
Ding P
(2021)
Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.
in Journal of experimental botany
He S
(2022)
DNA methylation dynamics during germline development.
in Journal of integrative plant biology
Hsieh PH
(2016)
Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues.
in Proceedings of the National Academy of Sciences of the United States of America
Johnson KC
(2015)
The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.
in Plant & cell physiology
Long J
(2021)
Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis.
in Science (New York, N.Y.)
Manavella PA
(2023)
Beyond transcription: compelling open questions in plant RNA biology.
in The Plant cell
Park K
(2016)
DNA demethylation is initiated in the central cells of Arabidopsis and rice.
in Proceedings of the National Academy of Sciences of the United States of America
Walker J
(2018)
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis.
in Nature genetics
| Description | 1. We found CG methylation is robustly maintained in the sperm and vegetative cells allowing methylation patterns to be accurately inherited across generations, and RdDM activity extends into heterochromatin in vegetative cells. 2. We reported the methylomes of Arabidopsis and rice central cells, and rice egg cell. We found active DNA demethylation in the central cell is the origin ofmaternal chromosome hypomethylation in the endosperm. 3. We find a sperm-specific histone variant H2B.8, responsible for sperm condensation in angiosperms. We further revealed that H2B.8 condense the sperm chromatin and nucleus via a phase separation mechanism. |
| Exploitation Route | Our findings contribute to further understanding of intergenerational epigenetic inheritance. The reported egg and central cell methylomes can be used by other researchers to identify imprinted genes and understand their imprinting mechanisms, both potentially useful for seed improvement. |
| Sectors | Agriculture Food and Drink Education |
| Description | BBSRC DTP Studentship |
| Amount | £90,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 09/2020 |
| Description | EMBO Young Investigator |
| Amount | € 15,000 (EUR) |
| Organisation | European Molecular Biology Organisation |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 01/2019 |
| End | 12/2022 |
| Description | European Research Council Starting Grant |
| Amount | € 1,500,000 (EUR) |
| Organisation | European Research Council (ERC) |
| Sector | Public |
| Country | Belgium |
| Start | 08/2018 |
| End | 08/2023 |
| Description | Gatsby Grant to Exceptional Researchers |
| Amount | £35,000 (GBP) |
| Organisation | Gatsby Charitable Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 07/2018 |
| End | 04/2019 |
| Description | Gatsby PhD Studentship |
| Amount | £107,494 (GBP) |
| Organisation | Gatsby Charitable Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2015 |
| End | 09/2019 |
| Description | JIC / CAS (Centre of Excellence in Plant and Microbial Science - CEPAMS) |
| Amount | £99,679 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2015 |
| End | 08/2017 |
| Description | John Innes Foundation PhD Studentship |
| Amount | £105,206 (GBP) |
| Organisation | John Innes Centre |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 08/2015 |
| End | 08/2018 |
| Title | Bisulfite and RNA sequencing library preparation using small number of plant cells |
| Description | We and our collaborators at University of Hamburg have modified the published animal single-cell bisulfite and RNA sequencing libary preparation protocols to prepare bisulfite and RNA sequencing libraries from as low as 20 Arabidopsis cells |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | Allow the obtainment of methylome and transcriptome from rare cells |
| Title | Isolation of plant cells via FACS |
| Description | We have developed robust method for protoplasting in Arabidopsis and isolating protoplasts via FACS |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Allows researchers to obtain cells of a specific cell/tissue type, in order to understand their transcriptome, genome or epigenome. |
| Description | Egg and central cell methylomes |
| Organisation | Seoul National University |
| Department | Department of Biological Sciences |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | I designed the experiment together with my collaborators, and I and my team did all the genome analysis. |
| Collaborator Contribution | UC Berkeley and Seoul National University isolated the egg and central cells from Arabidopsis, UC Berkeley and Tokyo Metropolitan University isolated these from rice, Hamburg University performed bisulfite sequencing library preparation |
| Impact | Park et al. 2016 PNAS 113(52):15138-15143 |
| Start Year | 2012 |
| Description | Egg and central cell methylomes |
| Organisation | Tokyo Metropolitan University |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | I designed the experiment together with my collaborators, and I and my team did all the genome analysis. |
| Collaborator Contribution | UC Berkeley and Seoul National University isolated the egg and central cells from Arabidopsis, UC Berkeley and Tokyo Metropolitan University isolated these from rice, Hamburg University performed bisulfite sequencing library preparation |
| Impact | Park et al. 2016 PNAS 113(52):15138-15143 |
| Start Year | 2012 |
| Description | Egg and central cell methylomes |
| Organisation | University of California, Berkeley |
| Department | Department of Plant and Microbial Biology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I designed the experiment together with my collaborators, and I and my team did all the genome analysis. |
| Collaborator Contribution | UC Berkeley and Seoul National University isolated the egg and central cells from Arabidopsis, UC Berkeley and Tokyo Metropolitan University isolated these from rice, Hamburg University performed bisulfite sequencing library preparation |
| Impact | Park et al. 2016 PNAS 113(52):15138-15143 |
| Start Year | 2012 |
| Description | Egg and central cell methylomes |
| Organisation | University of Hamburg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | I designed the experiment together with my collaborators, and I and my team did all the genome analysis. |
| Collaborator Contribution | UC Berkeley and Seoul National University isolated the egg and central cells from Arabidopsis, UC Berkeley and Tokyo Metropolitan University isolated these from rice, Hamburg University performed bisulfite sequencing library preparation |
| Impact | Park et al. 2016 PNAS 113(52):15138-15143 |
| Start Year | 2012 |
| Description | JIC-CAS CEPAMS grant |
| Organisation | Chinese Academy of Sciences |
| Department | Institute of Genetics & Developmental Biology |
| Country | China |
| Sector | Academic/University |
| PI Contribution | I came up with the idea and hypothesis, and designed the experimental strategy. Upon receiving the funding, I employed a postdoc who is performing the major epigenetics and biochemistry work for this joint project. |
| Collaborator Contribution | My partners in the Chinese Academy of Science bring the mass spectrometry expertise that is required for the joint project. |
| Impact | N/A |
| Start Year | 2015 |
| Description | Meiosis-specific TFIID in promoting recombination |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We found a TFIID component is meiocyte specifically expressed, and performed meiocyte extraction and RNA-seq with wildtype and mutants. |
| Collaborator Contribution | Identification of the allele and recombination phenotyping |
| Impact | This has led to a publication in Current Biology in 2019. Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col×Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics and immunocytology we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA-seq from purified meiocytes, we show that TAF4b expression is meiocyte-enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which acts directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor. |
| Start Year | 2017 |
| Description | Methylomes of megaspore mother cells |
| Organisation | National Laboratory of Genomics for Biodiversity |
| Country | Mexico |
| Sector | Public |
| PI Contribution | We designed the experiemnts together with our collaborator, prepared and sequenced the libraries, and analysed the data. |
| Collaborator Contribution | They isolated the megaspore mother cells from wild type Arabidopsis and mutants |
| Impact | A publication by mid 2018 |
| Start Year | 2015 |
| Description | Robust maintenance of CG methylation in pollen |
| Organisation | University of California, Berkeley |
| Department | Department of Plant and Microbial Biology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We designed and performed the experiments, and analysed data. |
| Collaborator Contribution | UC Berkeley contributed to data analysis. |
| Impact | Hsieh et al. 2016 PNAS 113(52):15132-15137 |
| Start Year | 2015 |
| Description | ASM poster |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | PhD student Billy Aldridge presented a poster on the JIC annual science meeting, which sparked lots of interest and discussion. He won the runner-up award, and an opportunity for presenting his research orally during the annual science meeting next year (2018) |
| Year(s) Of Engagement Activity | 2017 |
| Description | Interview about career pathways in science |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | In an interview filmed by the Communications Team at JIC, I talked about my career path and experiences, mainly targetting young people interested in science. The video was released on the International Women's Day in 2022, on JIC website (and Twitter) and YouTube. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.jic.ac.uk/blog/career-pathways-in-science/ |
| Description | Science Innovation Showcase |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | An event showcasing John Innes Centre science to industry, aiming to develop and promote new relationships between scientists and industry, breaking down any barriers and enabling productive collaborations. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.jic.ac.uk/news-and-events/whats-on/science-innovation-showcase/ |