Epigenetic regulation of plant reproductive development

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

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.

Publications

10 25 50
 
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.
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

 
Description Our study showed for the first time that a de novo DNA methylation pathway can be employed to regulate cell-specific gene expression and cellular development in plants. This highlights the potential of using this pathway to regulate gene expression for crop improvement, and also indicates the possible involvement of de novo methylation in animal development, which has applications in combatting human diseases. I have presented our result in a Science Innovation Showcase event open to the industries, which showed interest and I believe recognized the potential.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
 
Description BBSRC DTP Studentship
Amount £90,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
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 09/2018 
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 08/2018 
End 04/2019
 
Description Gatsby PhD Studentship
Amount £107,494 (GBP)
Organisation Gatsby Charitable Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2015 
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 09/2015 
End 08/2017
 
Description John Innes Foundation PhD Studentship
Amount £105,206 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 09/2015 
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 Not yet
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 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/