Nucleation of Polycomb silencing at FLC
Lead Research Organisation:
John Innes Centre
Department Name: Cell and Develop Biology
Abstract
The Dean group studies the control of flowering time in the reference plant, thalecress (Arabidopsis thaliana). Several flowering pathways converge to regulate a gene called FLC and variation in expression of this gene contributes enormously to natural variation in flowering time of Arabidopsis types collected from around the world. Winter conditions switch off expression of the FLC gene, removing the brake to flowering, and thus accelerating the flowering process. This induction of a plant's flowering process by exposure to the prolonged cold of winter is termed "vernalization." Genetic, molecular and computational analysis of vernalization in thalecress has shown it involves a cellular memory mechanism, one that also occurs during development of our own bodies. In the plant, cold switches off expression of FLC and this repressed state is maintained by Polycomb proteins that add methylation groups to proteins associated with FLC DNA. These modifications are passed from the mother to the daughter DNA strand to maintain the repressed state of the gene through the development as epigenetic regulation and similar mechanisms keep many thousands of genes switched off (silenced) during vertebrate development. A key question in the epigenetic field is what determines whether a specific gene becomes silenced or not.
Recent work in the Dean lab has made progress in this question through characterization of a change in the sequence of the FLC gene that blocks the silencing by cold. This then enabled the factor that binds to that specific region to be identified. Use of a tagged version of the factor then enabled isolation of a range of proteins that were in many cases unexpected and which suggested what might be involved in the silencing switch. This proposal aims to follow up these findings to fully describe the multiple factors required to specify a gene for epigenetic silencing. Understanding from a study such as this can provide concepts important to epigenetic regulation across many genomes.
Recent work in the Dean lab has made progress in this question through characterization of a change in the sequence of the FLC gene that blocks the silencing by cold. This then enabled the factor that binds to that specific region to be identified. Use of a tagged version of the factor then enabled isolation of a range of proteins that were in many cases unexpected and which suggested what might be involved in the silencing switch. This proposal aims to follow up these findings to fully describe the multiple factors required to specify a gene for epigenetic silencing. Understanding from a study such as this can provide concepts important to epigenetic regulation across many genomes.
Technical Summary
This proposal will investigate a central question in epigenetics -what factors specify a gene for Polycomb silencing? It will build on the recent identification of a single nucleotide polymorphism within the target gene that blocks Polycomb silencing in the well-characterized Polycomb switching system, cold-induced Arabidopsis FLC silencing. Knowledge of the DNA sequence required enabled identification of the binding protein and then proteomic identification of proteins that associate with that binding protein. This opens up experimental approaches to elucidate the mechanisms underlying what specifies Polycomb targets and what is required to epigenetically switch a locus from one chromatin state to another.
We will test the hypothesis that multiple factors determine Polycomb target selection and that their combined action synergize to nucleate Polycomb complexes, and thus switch the gene from an epigenetically active to a silent state. The specific DNA binding protein is VAL1 and its interacting partners include components of the Polycomb Repressive Complex 1 and the Apoptosis and Splicing Associated Protein (ASAP) complex. In turn the ASAP components interact with PHD proteins previously associated with the PRC2 complex, required at FLC for epigenetic switching. These protein interactions thus directly link DNA sequence specificity through to epigenetic switching via ASAP and PRC1.
The work will involve four interconnected experimental avenues aimed at mechanistically understanding how these functions link together. We will define the minimal sequence and VAL factor requirement for nucleation; establish the role of the ASAP complex; investigate how ASAP links through to VRN5 and VIN3 and test if Polycomb Repressive Complex 1 functions directly in FLC silencing. Our aim will be to fully integrate all the functions and understand how they lead to robust epigenetic switching.
We will test the hypothesis that multiple factors determine Polycomb target selection and that their combined action synergize to nucleate Polycomb complexes, and thus switch the gene from an epigenetically active to a silent state. The specific DNA binding protein is VAL1 and its interacting partners include components of the Polycomb Repressive Complex 1 and the Apoptosis and Splicing Associated Protein (ASAP) complex. In turn the ASAP components interact with PHD proteins previously associated with the PRC2 complex, required at FLC for epigenetic switching. These protein interactions thus directly link DNA sequence specificity through to epigenetic switching via ASAP and PRC1.
The work will involve four interconnected experimental avenues aimed at mechanistically understanding how these functions link together. We will define the minimal sequence and VAL factor requirement for nucleation; establish the role of the ASAP complex; investigate how ASAP links through to VRN5 and VIN3 and test if Polycomb Repressive Complex 1 functions directly in FLC silencing. Our aim will be to fully integrate all the functions and understand how they lead to robust epigenetic switching.
Planned Impact
Dissection of the mechanisms underlying epigenetic regulation is a very active area of biology. Indeed the global epigenetics market size was valued at USD 3.98 billion in 2014. Increasing prevalence of cancer is the key driver propelling the growth of the epigenetics market." (http://www.grandviewresearch.com/industry-analysis/epigenetics-market). Research on plant systems may also provide opportunities in agriculture and different mechanistic insights from biomedical research.
Important concepts relevant to gene expression generally are emerging from very different systems. The Dean lab has identified an excellent system in which to explore chromatin-based epigenetic mechanisms and the interaction of multiple components that synergize functionally to effect a switch. FLC regulation represents a system where different approaches can be combined to give a comprehensive view of the complexity and plasticity of epigenetic regulation. This will be of broad relevance to the biotechnology community, the pharmaceutical industry, particularly those involved in cancer research - and possibly also ageing research.
A clearer understanding of the molecular basis of switching mechanisms underpinning flowering/vernalization will inform strategies as to how to manipulate heading date, a key trait in breeding of many crops. The John Innes Centre is very unusual in combining basic biological research with crop-based studies. Groups interact on a daily basis, so results emerging from model species are quickly applied to crops such as Brassicas and cereals. Prof. Dean, collaboratively with Dr Judith Irwin (Dept. Crop Genetics, John Innes Centre) also has very good links with the plant breeding and biotechnology industries (Elsoms Seeds Ltd, Bejo Zaden BV and Bayer Crop Science), and there are frequent visits in both directions. The focus in the Dean/Irwin labs is manipulation of vernalization requirement and response - a key process in the production of many vegetable crops, broccoli, cauliflower, parsnips and carrots. Varieties of these vegetables are bred to ensure year round supply but the vagaries of winter temperatures and climate uncertainty tend to lead to gluts or shortages in production. Development of varieties less influenced by temperature but still producing in different seasons of the year would considerably reduce waste, potentially open up new production areas and increase efficiency of delivery. Ongoing funded collaborations with breeding companies (Elsoms Seeds Ltd) aim to translate this understanding into practical benefits.
The work will also contribute fundamental information that provides a framework of understanding for manipulation of developmental processes generally in less tractable but strategically important plants. The understanding emanating from epigenetic analysis in Arabidopsis is a good paradigm for how fundamental information informs generally and influences experimental strategies of a wide community of plant biologists.
Important concepts relevant to gene expression generally are emerging from very different systems. The Dean lab has identified an excellent system in which to explore chromatin-based epigenetic mechanisms and the interaction of multiple components that synergize functionally to effect a switch. FLC regulation represents a system where different approaches can be combined to give a comprehensive view of the complexity and plasticity of epigenetic regulation. This will be of broad relevance to the biotechnology community, the pharmaceutical industry, particularly those involved in cancer research - and possibly also ageing research.
A clearer understanding of the molecular basis of switching mechanisms underpinning flowering/vernalization will inform strategies as to how to manipulate heading date, a key trait in breeding of many crops. The John Innes Centre is very unusual in combining basic biological research with crop-based studies. Groups interact on a daily basis, so results emerging from model species are quickly applied to crops such as Brassicas and cereals. Prof. Dean, collaboratively with Dr Judith Irwin (Dept. Crop Genetics, John Innes Centre) also has very good links with the plant breeding and biotechnology industries (Elsoms Seeds Ltd, Bejo Zaden BV and Bayer Crop Science), and there are frequent visits in both directions. The focus in the Dean/Irwin labs is manipulation of vernalization requirement and response - a key process in the production of many vegetable crops, broccoli, cauliflower, parsnips and carrots. Varieties of these vegetables are bred to ensure year round supply but the vagaries of winter temperatures and climate uncertainty tend to lead to gluts or shortages in production. Development of varieties less influenced by temperature but still producing in different seasons of the year would considerably reduce waste, potentially open up new production areas and increase efficiency of delivery. Ongoing funded collaborations with breeding companies (Elsoms Seeds Ltd) aim to translate this understanding into practical benefits.
The work will also contribute fundamental information that provides a framework of understanding for manipulation of developmental processes generally in less tractable but strategically important plants. The understanding emanating from epigenetic analysis in Arabidopsis is a good paradigm for how fundamental information informs generally and influences experimental strategies of a wide community of plant biologists.
People |
ORCID iD |
Caroline Dean (Principal Investigator) |
Publications
Berry S
(2017)
Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression.
in Genes & development
Bloomer RH
(2020)
The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2.
in Proceedings of the National Academy of Sciences of the United States of America
Costa S
(2019)
Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC.
in Biochemical Society transactions
Dean C
(2017)
What holds epigenetic memory?
in Nature reviews. Molecular cell biology
Duncan S
(2017)
Single Molecule RNA FISH in Arabidopsis Root Cells.
in Bio-protocol
Fiedler M
(2022)
Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control.
in Cell reports
Franco-Echevarría E
(2023)
Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing.
in Genes & development
Franco-Echevarría E
(2022)
Plant vernalization proteins contain unusual PHD superdomains without histone H3 binding activity.
in The Journal of biological chemistry
Ietswaart R
(2017)
Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation.
in Cell systems
Mattick JS
(2023)
Long non-coding RNAs: definitions, functions, challenges and recommendations.
in Nature reviews. Molecular cell biology
Description | Core epigenetic switching mechanisms have proven difficult to elucidate due to the complex molecular feedbacks involved. Over the last eight years, we have combined molecular investigations into the epigenetic silencing of a single Arabidopsis locus, FLC, with mathematical modelling. This has allowed us to conceptualise the distinct phases of the silencing process into a cis-based, digital switching mechanism providing principles that are conserved across a wide range of organisms. Local transcription needs to be repressed before silencing can occur. Recruitment of a PRC2 complex by PRC2-accessory proteins to a specific site in the locus leads to a stochastic switch of each allele independently to a metastably silenced state. Spreading of the Polycomb complex across the body of the gene then results in stable epigenetic silencing. |
Exploitation Route | This work has the potential to open many new horizons in the manipulation of Polycomb switching mechanisms, ranging from cancer therapeutics to agriculture. |
Sectors | Agriculture, Food and Drink,Healthcare |
URL | http://www.jic.ac.uk/staff/caroline-dean/ |
Description | Breeding companies are using the information on nucleation of FLC silencing in strategies for molecular breeding to generate climate-ready crops |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink |
Impact Types | Societal |
Description | Biological physics of protein clustering in epigenetic memory and transcriptional control |
Amount | £718,575 (GBP) |
Funding ID | EP/T00214X/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2019 |
End | 03/2022 |
Description | GCRF databases and Resources phase 2 |
Amount | £98,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2017 |
End | 07/2018 |
Description | Mechanistic basis of nucleation and spreading underlying a Polycomb-mediated epigenetic switch (EPISWITCH) |
Amount | € 2,100,000 (EUR) |
Funding ID | 833254 |
Organisation | European Research Council (ERC) |
Sector | Public |
Country | Belgium |
Start | 09/2019 |
End | 09/2024 |
Description | Nuclear organization at FLC |
Organisation | Uppsala University |
Country | Sweden |
Sector | Academic/University |
PI Contribution | We are supplying the mechanistic information on FLC regulation |
Collaborator Contribution | Dr Stefanie Rosa is continuing work started as a post-doc in Norwich, to determine changes in FLC nuclear position at different phases of the epigenetic silencing process |
Impact | No outputs yet |
Start Year | 2020 |
Description | Chair and invited lecture at the EMBO 2016 meeting in Mannheim, Germany. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Caroline Dean chaired and gave an invited lecture entitled: "Antisense-mediated chromatin silencing at FLC" at the EMBO 2016 meeting in Mannheim, Germany. |
Year(s) Of Engagement Activity | 2016 |
Description | Invited lecture at an EMBO workshop in Stockholm. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Caroline Dean gave an invited lecture, entitled: "Antisense-mediated chromatin silencing at FLC" at an EMBO workshop in Stockholm on 12 June 2016. |
Year(s) Of Engagement Activity | 2016 |
Description | Invited speaker at Peking University, Beijing, China |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean was invited to speak at Peking University, Beijing, China, on the 1st June. Her seminar was entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited speaker at Sustech Shenzhei, China. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean was invited to speak at Sustech Shenzhei, China on the 28th May. Her seminar was entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited speaker at Tsinghua University, China |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean was invited to speak at Tsughua University, China, on the 30th May. Her seminar was entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited speaker at Wellcome Trust Plant 'Genomes in a Changing Environment' meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean gave the keynote lecture on the 24th October 2018 at the Wellcome Trust Hixton Hall Plant Genomes in a Changing Environment meeting. Her talk was entitled: 'Adapting to different winters'. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited speaker at international Arabidopsis meeting in Turku Finland |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | On the 27th June Caroline gave an invited talk at the international Arabidopsis conference in Turku, Finland entitled: 'Sensing and remembering winter'. |
Year(s) Of Engagement Activity | 2018 |
Description | Keynote Lecture at International Congress of Genetics, Iguassu, Brazil |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | ON the 11th September 2018 Caroline Dean gave the Keynote Lecture at the International Congress of Genetics, Iguassu, Brazil, entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | Keynote Lecture on epigenetics at the Netherlands Cancer Institute (NKI). |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Dean gave the Keynote lecture at the Dutch Chromatin meeting at the Netherlands Cancer Institute (NKI) on the 2nd November 2018. Translational talks (outside the field of plant science) increase the impact and application of GEN Science. Her talk was entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | McClintock Lecture Cold Spring Harbor Laboratory |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean gave the Barbara McClintock Lecture at Cold Spring Harbor Laboratory NY on chromatin regulation and evolutionary adaptation. The talk stimulated discussion and questions. |
Year(s) Of Engagement Activity | 2018 |
URL | http://cshlwise.org/institutional-events/mcclintock-lectures/ |
Description | Non-resident faculty participation at SALK Institute annual retreat San Diego |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Prof Caroline Dean participated as non-resident faculty at the SALK Institute annual retreat in San Diego, from 16th-22nd March 2016. |
Year(s) Of Engagement Activity | 2016 |
Description | Seminar as part of a College de France conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This was a virtual meeting discussing how the environment influences cellular behaviour |
Year(s) Of Engagement Activity | 2021 |
Description | Seminar as part of the EC COST Plant Chromatin meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This is an active group of chromatin researchers funded by a COST project and I was the invited speaker to their annual meeting. |
Year(s) Of Engagement Activity | 2021 |
Description | Seminar at EMBL Epigenetics & Chromatin conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This was a virtual presentation to a diverse audience on the mechanistic basis of epigenetic switching |
Year(s) Of Engagement Activity | 2021 |
Description | Seminar given at Gatersleben IPK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Caroline Dean gave a seminar at Gatersleben IPK on the 20th November entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |
Description | Seminar given at University of Rennes entitled: 'Epigenetic switching and antisense transcription'. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | On the 14th May 2018 Caroline Dean gave a seminar at the University of Rennes entitled: 'Epigenetic switching and antisense transcription'. |
Year(s) Of Engagement Activity | 2018 |