Project acronym ENVGENE
Project Dissection of environmentally-mediated epigenetic silencing
Researcher (PI) Caroline Dean
Host Institution (HI) JOHN INNES CENTRE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary We intend to achieve a step change in our understanding of the mechanistic basis of epigenetic regulation. We will capitalize on a plant epigenetic silencing system, vernalization, which has many features that allow the complete dissection of different facets of epigenetic regulation. In addition, the silencing is quantitatively modulated by the environment enabling dissection of how external cues mediate epigenetic silencing. We will combine genetics, molecular biology and biochemical approaches with computational modelling to allow us to translate the extensive nuts and bolts information into an understanding of how the engine works. A particular strength of modelling will be its predictive nature and ability to distinguish between key components and those with subsidiary or redundant roles. The system we will use is vernalization, the cold-induced Polycomb-silencing of the target locus, FLC. We will dissect the many phases of vernalization: the triggering of FLC repression by prolonged cold; the nucleation and epigenetic stability of chromatin changes at FLC; and the spreading of the silencing yet spatial restriction to FLC. Our goal will be a full understanding of the complexity involved in the epigenetic silencing of this locus, described in a quantitative model that reveals how the silencing is induced by temperature and how individual components of the silencing network are integrated into a robust whole. This ambitious goal, which will uncover fundamental concepts important to gene regulation in many organisms, will be achieved through a tight integration of molecular analysis and computational modelling, enabling efficient cycling between experimentation, prediction and validation.
Summary
We intend to achieve a step change in our understanding of the mechanistic basis of epigenetic regulation. We will capitalize on a plant epigenetic silencing system, vernalization, which has many features that allow the complete dissection of different facets of epigenetic regulation. In addition, the silencing is quantitatively modulated by the environment enabling dissection of how external cues mediate epigenetic silencing. We will combine genetics, molecular biology and biochemical approaches with computational modelling to allow us to translate the extensive nuts and bolts information into an understanding of how the engine works. A particular strength of modelling will be its predictive nature and ability to distinguish between key components and those with subsidiary or redundant roles. The system we will use is vernalization, the cold-induced Polycomb-silencing of the target locus, FLC. We will dissect the many phases of vernalization: the triggering of FLC repression by prolonged cold; the nucleation and epigenetic stability of chromatin changes at FLC; and the spreading of the silencing yet spatial restriction to FLC. Our goal will be a full understanding of the complexity involved in the epigenetic silencing of this locus, described in a quantitative model that reveals how the silencing is induced by temperature and how individual components of the silencing network are integrated into a robust whole. This ambitious goal, which will uncover fundamental concepts important to gene regulation in many organisms, will be achieved through a tight integration of molecular analysis and computational modelling, enabling efficient cycling between experimentation, prediction and validation.
Max ERC Funding
2 450 000 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym FastBio
Project A genomics and systems biology approach to explore the molecular signature and functional consequences of long-term, structured fasting in humans
Researcher (PI) Antigoni DIMA
Host Institution (HI) BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING
Call Details Starting Grant (StG), LS2, ERC-2016-STG
Summary Dietary intake has an enormous impact on aspects of human health, yet scientific consensus about how what we eat affects our biology remains elusive. To address the complex biological impact of diet, I propose to apply an unconventional, ‘humans-as-model-organisms’ approach to compare the molecular and functional effects of a highly structured dietary regime, specified by the Eastern Orthodox Christian Church (EOCC), to the unstructured diet followed by the general population. Individuals who follow the EOCC regime abstain from meat, dairy products and eggs for 180-200 days annually, in a temporally-structured manner initiated in childhood. I aim to explore the biological signatures of structured vs. unstructured diet by addressing three objectives. First I will investigate the effects of the two regimes, and of genetic variation, on higher-level phenotypes including anthropometric, physiological and biomarker traits. Second, I will carry out a comprehensive set of omics assays (metabolomics, transcriptomics, epigenomics and investigation of the gut microbiome), will associate omics phenotypes with genetic variation, and will integrate data across biological levels to uncover complex molecular signatures. Third, I will interrogate the functional consequences of dietary regimes at the cellular level through primary cell culture. Acute and long-term effects of dietary intake will be explored for all objectives through a two timepoint sampling strategy. This proposal therefore comprises a unique opportunity to study a specific perturbation (EOCC structured diet) introduced to a steady-state system (unstructured diet followed by the general population) in a ground-breaking human systems biology type of study. This approach brings together expertise from genomics, computational biology, statistics, medicine and epidemiology. It will lead to novel insights regarding the potent signalling nature of nutrients and is likely to yield results of high translational value.
Summary
Dietary intake has an enormous impact on aspects of human health, yet scientific consensus about how what we eat affects our biology remains elusive. To address the complex biological impact of diet, I propose to apply an unconventional, ‘humans-as-model-organisms’ approach to compare the molecular and functional effects of a highly structured dietary regime, specified by the Eastern Orthodox Christian Church (EOCC), to the unstructured diet followed by the general population. Individuals who follow the EOCC regime abstain from meat, dairy products and eggs for 180-200 days annually, in a temporally-structured manner initiated in childhood. I aim to explore the biological signatures of structured vs. unstructured diet by addressing three objectives. First I will investigate the effects of the two regimes, and of genetic variation, on higher-level phenotypes including anthropometric, physiological and biomarker traits. Second, I will carry out a comprehensive set of omics assays (metabolomics, transcriptomics, epigenomics and investigation of the gut microbiome), will associate omics phenotypes with genetic variation, and will integrate data across biological levels to uncover complex molecular signatures. Third, I will interrogate the functional consequences of dietary regimes at the cellular level through primary cell culture. Acute and long-term effects of dietary intake will be explored for all objectives through a two timepoint sampling strategy. This proposal therefore comprises a unique opportunity to study a specific perturbation (EOCC structured diet) introduced to a steady-state system (unstructured diet followed by the general population) in a ground-breaking human systems biology type of study. This approach brings together expertise from genomics, computational biology, statistics, medicine and epidemiology. It will lead to novel insights regarding the potent signalling nature of nutrients and is likely to yield results of high translational value.
Max ERC Funding
1 500 000 €
Duration
Start date: 2017-06-01, End date: 2022-05-31
Project acronym MaintainMeth
Project Quantitative analysis of DNA methylation maintenance within chromatin
Researcher (PI) Daniel ZILBERMAN
Host Institution (HI) JOHN INNES CENTRE
Call Details Consolidator Grant (CoG), LS2, ERC-2016-COG
Summary Cytosine methylation is a chemical modification that is precisely copied when DNA is replicated. Because methylation can regulate gene expression, accurate reproduction of DNA methylation patterns is essential for plant and animal development and for human health. The enzymes that maintain DNA methylation have to work within chromatin, and particularly to contend with nucleosomes – tight complexes of DNA and histone proteins. How methylation of nucleosomal DNA is maintained remains unknown, and even the simple matter of whether nucleosomes hinder or promote methylation is controversial.
My laboratory’s recent work with DDM1 – an ancient protein conserved between plants and animals that can move nucleosomes – and linker histone H1, which binds to nucleosomes and the intervening ‘linker’ DNA, has allowed us to formulate a model wherein movement of nucleosomes by DDM1 dislodges H1 and allows methyltransferases to access the DNA. Furthermore, this work revealed the existence of unknown factors required to maintain DNA methylation. My laboratory also discovered that DNA methylation influences nucleosome placement, thereby demonstrating that the interaction between DNA methylation and nucleosomes is bidirectional.
My goal is now to deeply understand the connected processes of maintenance methylation and nucleosome placement. This will be achieved through three interconnected research strands:
1) Elucidation of how DNA methylation is maintained within chromatin.
2) Identification of new DNA methylation maintenance factors.
3) Determination of how DNA methylation influences nucleosomes in vivo.
Our ultimate output will be the creation of a mathematical model of DNA methylation maintenance that will incorporate the bidirectional interactions between methylation and nucleosomes. This breakthrough will revolutionize research in the field by permitting the development of precise, quantitative hypotheses about the maintenance and function of DNA methylation within chromatin.
Summary
Cytosine methylation is a chemical modification that is precisely copied when DNA is replicated. Because methylation can regulate gene expression, accurate reproduction of DNA methylation patterns is essential for plant and animal development and for human health. The enzymes that maintain DNA methylation have to work within chromatin, and particularly to contend with nucleosomes – tight complexes of DNA and histone proteins. How methylation of nucleosomal DNA is maintained remains unknown, and even the simple matter of whether nucleosomes hinder or promote methylation is controversial.
My laboratory’s recent work with DDM1 – an ancient protein conserved between plants and animals that can move nucleosomes – and linker histone H1, which binds to nucleosomes and the intervening ‘linker’ DNA, has allowed us to formulate a model wherein movement of nucleosomes by DDM1 dislodges H1 and allows methyltransferases to access the DNA. Furthermore, this work revealed the existence of unknown factors required to maintain DNA methylation. My laboratory also discovered that DNA methylation influences nucleosome placement, thereby demonstrating that the interaction between DNA methylation and nucleosomes is bidirectional.
My goal is now to deeply understand the connected processes of maintenance methylation and nucleosome placement. This will be achieved through three interconnected research strands:
1) Elucidation of how DNA methylation is maintained within chromatin.
2) Identification of new DNA methylation maintenance factors.
3) Determination of how DNA methylation influences nucleosomes in vivo.
Our ultimate output will be the creation of a mathematical model of DNA methylation maintenance that will incorporate the bidirectional interactions between methylation and nucleosomes. This breakthrough will revolutionize research in the field by permitting the development of precise, quantitative hypotheses about the maintenance and function of DNA methylation within chromatin.
Max ERC Funding
2 749 962 €
Duration
Start date: 2017-04-01, End date: 2022-03-31
Project acronym REVOLUTION
Project RNA silencing in regulation and evolution
Researcher (PI) David Baulcombe
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Small RNA is a specificity determinant of silencing mechanisms that can target RNA through base pairing to affect RNA stability and translation. This targeting process, directly or indirectly, can also target DNA and chromatin to introduce epigenetic modifications. In plants there are many hundreds of thousands - of different small silencing RNAs (sRNAs) produced from many thousands of loci. These sRNAs have enormous potential to influence genetic and epigenetic regulation because, from analysis of transgenes, it is clear that RNA silencing can have diverse effects. There can be RNA-mediated signalling between cells and complex interaction networks of RNA molecules with positive feedback and amplification loops. In addition there can be epigenetic effects that, once induced, can persist between generations. In REVOLUTION the aim is to find out which of the endogenous sRNAs have the various RNA silencing properties revealed by transgenes. The aim is then to integrate these findings into a systems level understanding of regulation and evolution in Arabidopsis. The role of these sRNA systems will be investigated in plants subjected to hormone and stress treatments. We shall also investigate the role of these sRNAs in natural variation between genotypes of plant and their effect in hybrids between these plants. In the final stages of the work it is intended to explore the various effects of endogenous sRNAs in plants other than Arabidopsis including tomato. This work will provide a new level of understanding of the mechanisms affecting gene expression in plants. This fundamental new understanding will affect crop science through conventional breeding and genetic engineering. In addition because RNA silencing takes place in animals including vertebrates there will be relevance of this work beyond plants.
Summary
Small RNA is a specificity determinant of silencing mechanisms that can target RNA through base pairing to affect RNA stability and translation. This targeting process, directly or indirectly, can also target DNA and chromatin to introduce epigenetic modifications. In plants there are many hundreds of thousands - of different small silencing RNAs (sRNAs) produced from many thousands of loci. These sRNAs have enormous potential to influence genetic and epigenetic regulation because, from analysis of transgenes, it is clear that RNA silencing can have diverse effects. There can be RNA-mediated signalling between cells and complex interaction networks of RNA molecules with positive feedback and amplification loops. In addition there can be epigenetic effects that, once induced, can persist between generations. In REVOLUTION the aim is to find out which of the endogenous sRNAs have the various RNA silencing properties revealed by transgenes. The aim is then to integrate these findings into a systems level understanding of regulation and evolution in Arabidopsis. The role of these sRNA systems will be investigated in plants subjected to hormone and stress treatments. We shall also investigate the role of these sRNAs in natural variation between genotypes of plant and their effect in hybrids between these plants. In the final stages of the work it is intended to explore the various effects of endogenous sRNAs in plants other than Arabidopsis including tomato. This work will provide a new level of understanding of the mechanisms affecting gene expression in plants. This fundamental new understanding will affect crop science through conventional breeding and genetic engineering. In addition because RNA silencing takes place in animals including vertebrates there will be relevance of this work beyond plants.
Max ERC Funding
2 298 433 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym SCG
Project Systematic Chemical Genetic Interrogation of Biological Networks
Researcher (PI) Michael David Tyers
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Recent genome-scale studies have revealed the massive redundancies and functional interconnectivities encoded by the genome. For example, the budding yeast Saccharomyces cerevisiae is predicted to harbor 200,000 synthetic lethal interactions. This genetic density has profound implications for both understanding the architecture of living systems and drug discovery. In particular, the dense connections of biological networks mandate a multi-node strategy to selectively manipulate any given biological response, whether it be to probe system level properties or for therapeutic intervention in human disease. By analogy to Ehrlich s magic bullet concept, we term this approach the magic shotgun . We propose to systematically identify chemical-genetic interactions that selectively disrupt any specific mutant genotype and chemical-chemical interactions that selectively kill pathogenic species. Our five main objectives are: (i) construct a comprehensive Chemical Genetic Matrix (CGM) of small molecule-gene interactions in order to predict chemical synergies and manipulate network function in a species-specific manner; (ii) elaborate the CGM with a set of ~5,000 yeast bioactive molecules derived from high throughput/high content screens; (iii) identify small molecule combinations that modulate stem cell and cancer cell renewal and differentiation; (iv) define compound mechanisms of action by functional genomics; (v) integrate chemical-genetic, genetic and protein interaction datasets to predict gene function, small molecule targets and network properties. This research will cross-connect genetic pathways through chemical space, identify species-specific combinations of agents as therapeutic leads and provide a repository of small molecule probes for cell biological and systems-level analysis. The principles developed through the course of this work will raise our understanding of biological networks and help establish a new approach to drug discovery.
Summary
Recent genome-scale studies have revealed the massive redundancies and functional interconnectivities encoded by the genome. For example, the budding yeast Saccharomyces cerevisiae is predicted to harbor 200,000 synthetic lethal interactions. This genetic density has profound implications for both understanding the architecture of living systems and drug discovery. In particular, the dense connections of biological networks mandate a multi-node strategy to selectively manipulate any given biological response, whether it be to probe system level properties or for therapeutic intervention in human disease. By analogy to Ehrlich s magic bullet concept, we term this approach the magic shotgun . We propose to systematically identify chemical-genetic interactions that selectively disrupt any specific mutant genotype and chemical-chemical interactions that selectively kill pathogenic species. Our five main objectives are: (i) construct a comprehensive Chemical Genetic Matrix (CGM) of small molecule-gene interactions in order to predict chemical synergies and manipulate network function in a species-specific manner; (ii) elaborate the CGM with a set of ~5,000 yeast bioactive molecules derived from high throughput/high content screens; (iii) identify small molecule combinations that modulate stem cell and cancer cell renewal and differentiation; (iv) define compound mechanisms of action by functional genomics; (v) integrate chemical-genetic, genetic and protein interaction datasets to predict gene function, small molecule targets and network properties. This research will cross-connect genetic pathways through chemical space, identify species-specific combinations of agents as therapeutic leads and provide a repository of small molecule probes for cell biological and systems-level analysis. The principles developed through the course of this work will raise our understanding of biological networks and help establish a new approach to drug discovery.
Max ERC Funding
2 400 000 €
Duration
Start date: 2009-08-01, End date: 2014-07-31
