Nuclear organization of the Polycomb target FLC during the cold-induced epigenetic silencing of vernalization

Epigenetic regulation is the maintenance of specific gene expression states in the absence of the initial regulator over many cell generations, and sometimes transgenerationally. It is profoundly important for correct growth, development and environmental response in most organisms. In many cases the molecular basis of epigenetic regulation is associated with modification of chromatin, the methylation of the DNA or post-translational modification of the associated histones. For example, an epigenetic silencing mechanism central to control of cell differentiation, morphogenesis and developmental timing involves the so-called 'Polycomb complexes', a set of protein complexes that add methylation groups to a particular residue on the amino-terminal tail of histone 3. This 'mark' then attracts other silencing proteins that keep the gene switched off. Non-coding RNAs often recruit the Polycomb proteins to their specific targets but the exact mechanisms determining the specificity of their action is still being actively dissected. The 'marks' laid down on the chromatin need to be copied to the daughter chromatin strand every time a cell divides. A feature that may be very important for maintenance of the epigenetically silenced state is 'storage' of the targets in certain places in the nucleus, where all similarly regulated genes are collected. This nuclear re-positioning upon epigenetic silencing has been extensively characterized in the case of inactivation of one of the X-chromosomes in female mammals, but emerging data in many other systems suggests this is generally very important for epigenetic regulation. How a change in nuclear position ties in with all the other changes that occur is still not clear because it is often hard to study all the questions on one epigenetically silenced target. Over the last 15 years the Dean laboratory has studied the epigenetic silencing of the gene (called FLC) encoding an important repressor of flowering in plants in a process called vernalization. The very long period of cold experience during winter slowly but surely shuts off expression of this gene and this shut-down is remembered during the subsequent spring and summer, allowing the plants to flower in favourable conditions. Unlike many mammalian systems the plant system has the advantage that extensive genetic analysis can be combined with molecular, computational and cell biology techniques. This has resulted in the regulation of FLC being considered as the paradigm for environmentally-mediated epigenetic regulation. We want to build on this advantage and exploit a new experimental technique to observe changes in the nuclear organization of FLC during the cold-induced epigenetic silencing process involved in vernalization. The new information on nuclear organization and chromatin interactions, at different phases of the vernalization process, will be integrated with the other mechanistic information through analysis of mutants and specific transgenic lines. The results emerging from this work will allow us to integrate the importance of changes in nuclear organization with dynamic changes in histone 'mark' accumulation, non-coding RNA production and the cell autonomous epigenetic switching that underlies vernalization. It will also provide important conclusions for understanding more generally how nuclear organization is interconnected with epigenetic regulation.

An emerging theme in epigenetic regulation is the importance of physical position in the nucleus. New genomic and imaging technologies, including live cell imaging, have revealed the existence of nuclear territories and dynamic co-localization of similarly regulated chromosomal regions. The Dean laboratory has been studying the process of vernalization, a classic example of environmentally-induced epigenetic regulation. In Arabidopsis thaliana (Arabidopsis), vernalization involves a suppression of expression of the floral repressor FLC by prolonged cold and epigenetic maintenance of the repression through the rest of vegetative development. We have recently begun to investigate whether nuclear organization plays any role in vernalization. We chose to address this question by exploiting live cell imaging in Arabidopsis using an FLC-lacO array combined with LacI-YFP. Our recent unpublished data suggest that an aspect of nuclear organization, involving a clustering of FLC loci within the nucleus could be an important component of the vernalization epigenetic silencing mechanism. The success of this live imaging provides a rare opportunity to combine our extensive understanding from molecular, genetic and computational techniques with the dissection of the importance of nuclear organization in Polycomb silencing in plants. We will further develop the FLC-lacO system by characterizing additional lines and then exploring which genetic components are required for the observed FLC-lacO cold-induced clustering. We will investigate any role for the different non-coding transcripts associated with FLC epigenetic silencing; determine if clustering is a manifestation of increased nucleation during the cold; ask if the clustering is epigenetically stable. We will also explore if the clustering is limited to association of FLC loci or whether it includes other Polycomb-regulated targets and then analyze the interactions of FLC more generally.

Vernalization is an important trait in many crop species, and the Dean group has led the field in research aimed at understanding the molecular mechanisms underlying it. The John Innes Centre is very unusual in combining basic biological research with crop-based studies. Thus, there are groups with whom we interact on a daily basis, who will use the results emerging from model species to apply to crops such as Brassicas and cereals. The John Innes Centre, led by the crop scientists, also has very good links with the plant breeding and biotechnology industries, and there are frequent visits in both directions. The work leading up to this proposal has shown that vernalization is a classic example of an epigenetic phenomenon - in which developmental fate is altered in a heritable way that does not involve changes in the DNA sequence. Epigenetics is assuming great importance in a wide variety of developmental fields and in understanding many human diseases. Vernalization offers a particularly simple and powerful model for studying fundamental epigenetic mechanisms, and knowledge gained from these studies may well inform research and potential therapies for human health in the future.

The research in this proposal will thus have impact in three different areas:
Firstly, it will provide fundamental information on epigenetic regulation underpinning developmental and environmental processes in plants. This knowledge will affect the direction of research of many researchers in many plant systems. It will provide a framework of understanding that will greatly facilitate dissection of epigenetic processes in less tractable but strategically important plants. Our understanding of the flowering network underlying the control and variation in flowering in Arabidopsis would be a good paradigm for how we see this fundamental information trickling through and influencing a very wide community of plant biologist.
Secondly, since the epigenetic mechanisms show remarkable conservation the concepts emerging from this research are likely to influence epigenetic research across a broad range of organisms. Vernalization represents a system where different approaches can be combined to give a comprehensive view of the complexity and importance of dynamics behind environmentally-mediated epigenetic regulation. The volume of invitations of the PIs to speak at general conferences reinforces this view.
Thirdly, a clearer understanding of the molecular basis of vernalization will inform strategies as to how to manipulate the timing of the transition to flowering, a key trait in breeding of many crops. The focus in the Dean lab 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 tends 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. We have ongoing collaborations with breeding companies aiming to translate this understanding into practical benefits.