Bilateral BBSRC-SFI: Characterization of a novel Polycomb group protein complex and its effects on the plant epigenome

The DNA in our cells is packaged on proteins called histones. Recently it has become clear that the histone proteins can be modified in many different ways, for example by addition of methyl groups, and that this can affect the activity of genes nearby. These changes in the histone proteins - often termed epigenetic marks - are important not only because they affect gene activity, but also because in some cases they are inherited through cell division. Intense research focus on the histone proteins has revealed that cells contain sophisticated machinery not only to "write" epigenetic marks, but also to read them, i.e. recognise and interpret them to produce an output such as turning a gene off. In addition, there are "erasers" that can remove specific marks and reverse their effects. One of the most important histone writers are the Polycomb group (PcG) proteins, which control many aspects of development in animals and plants and are thought to provide cells with a stable memory of important events. For example, in plants the PcG proteins help plant flower at the right time of year by giving cells a memory of whether or not winter has occurred. During winter the cold temperatures result in certain genes involved in flowering being switched off and the PcG proteins are important in making sure that cells "remember" to keep these genes off when temperatures increase during spring and summer. For a long time it was a complete mystery how PcG proteins caused these stable memories. In the last ten years there have been major advances. In particular, it has been found that a group of PcG proteins, called PRC2, act together as an enzyme which methylates a specific amino acid on one of the four histone proteins that package DNA. Furthermore, technical developments in sequencing mean that we can now identify which genes in an organism are modified in this way, and how this relates to their activity. Because PcG proteins control genes involved in many economically important traits (flowering, seed size, and the viability of hybrids for example) it is important to know how the activity of the PRC2 is regulated.
The starting point for the present proposal was our discovery of several proteins, called ALP, which we found from genetic evidence which suggested that they act oppositely to the PcG and are involved in switching genes on. We later found, somewhat to our surprise, that the ALP proteins and the PRC2 PcG proteins act together in a large multiprotein complex. We think that when the ALP proteins associate with the PRC2 proteins they inhibit their activity so that the normal role of PcG in repressing gene activity is overcome. A further surprise was that the ALP1 protein turns out to be related to proteins called transposases which help parasitic elements called transposons to proliferate in plant and animal genomes. Because the ALP proteins are widely conserved in plants, including cereals, we think they could provide a useful tool to alter the epigenetic marks in plants and ultimately to modify useful agricultural traits. In order to do this, we need to know what effect ALP proteins have on PRC2 proteins, which genes they target, and what effects they have on the distribution of epigenetic marks over the genome. We have developed many of the genetic resources necessary to do this in our earlier work. We have also uncovered an unusual effect of ALP proteins on plants ability to perceive winter (the vernalization response) and wish to investigate whether this is a result of ALP proteins altering epigenetic marks at genes important for vernalization.
We propose to conduct the research outlined in this application as a partnership between our laboratories at the University of Edinburgh and Trinity College Dublin, respectively. Our two groups have complementary research strengths and expertise and we believe that, as a team, we can successfully address questions that could not be answered by one group alone.

Polycomb-group (PcG) proteins are key regulators of development in higher eukaryotes. In plants, they control numerous agronomically important traits, including the vernalization response, endosperm proliferation, flowering time and the responses to biotic and abiotic stresses. Although much has been learned about the molecular function of PcG proteins in recent years, how their activities are regulated in a developmental context has remained largely elusive. We recently described ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) as a novel, plant-specific accessory component of the Polycomb Repressive Complex 2 (PRC2). Further (unpublished) work resulted in the identification of ALP2, which directly interacts with ALP1. While our data suggest that ALP1/ALP2 inhibit PRC2 activity, the underlying molecular mechanism remains largely unknown. The overall aim of this proposal is to find out how the ALP proteins affect PRC2 activity and what the consequences are for the epigenome. Furthermore, we will test the hypothesis that alp mutations cause epigenetic changes in the vernalization response, possibly through effects on the DNA methylome. The two teams involved will provide complementary skills with the Goodrich group providing resources and expertise for analysing ALP-PRC2 activity and the Wellmer group expertise in genomics. Since the ALP proteins are conserved throughout angiosperms, the results will be important as a potential means for manipulating the epigenome in e.g. cereals. The results will also be of broad interest for evolutionary biologist, as the ALP1 protein has evolved by domestication of a former transposase protein.

The proposed project addresses an important question in biology: how is the epigenetic control of gene expression regulated in response to developmental and environmental cues? Because epigenetics promises advances in diverse fields ranging from cancer to hybrid vigour and virus resistance in plants, answering this question will have major implications not only for basic science but also for translational research and the development of applications in medicine and agriculture.
To address this key question we propose a bilateral collaboration between two groups that have complementary research skills and expertise. By identifying novel regulators of the core epigenetic machinery in plants and animals the work is a step in our ability to manipulate the epigenome and alter valuable traits such as flowering time and seed size. Although we do not expect to acquire an immediate marketable product during the project period, we will explore implementation strategies for our research throughout the project. Findings from the proposed research will be particularly attractive to agribusinesses that deliver genetically optimized crops, and we have devised a strategy to engage with companies in this sector to maximize the translational potential or our work. Because our laboratories have not previously collaborated, the project will also allow a transfer of knowledge and resources, which will enhance the training and research capabilities aof two leading European universities and strengthen the research ties between the UK and Ireland.
In this project, impact will be mainly delivered through a combination of basic research, which will inform and underpin related work in the area of (plant) epigenetics, as well as through training of staff and public engagement throughout the lifetime of the grant. Specifically, impact will be achieved as follows:

Basic research: We will investigate how Polycomb Group proteins are regulated by interacting proteins and functionally characterize the latter proteins using a wide range of state-of-the-art methods. Because these proteins are involved in regulating agriculturally important traits such as vernalization, our results will likely have direct implications for the discovery of new avenues for crop improvement.

Training of staff: Through the training of postdoctoral fellows, research assistants as well as Ph.D. and undergraduate students working in our laboratories, we will contribute to educating the next generation of scientists who will acquire the skill set necessary to pursue careers in either academ-ia, industry or government.

Public engagement: Impact will be delivered through a range of public information events where we will present our research project and its results. These include, among others, activities in schools, universities and science festivals such as the Edinburgh International Science Festival.

The beneficiaries of the proposed work will be:

a) scientific community: through new findings in an important area of biology and the generation of valuable datasets.

b) general public: through a greater understanding of plant biology and the regulation of gene expression as well as through insights into how research is being conducted.

c) university sector: through the improvement of infrastructure, increased resources, and a higher training and teaching potential.

d) undergraduate and postgraduate students: through training and education by experienced and highly skilled scientists and the direct involvement in state-of-the-art research projects.

e) economy in the UK/Ireland: through the training of highly skilled scientists with transferable skills.

f) global economy: through increased revenue from sales of novel cultivars developed based on an improved understanding of plant biology.