Project acronym BEEHIVE
Project Bridging the Evolution and Epidemiology of HIV in Europe
Researcher (PI) Christopher Fraser
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary The aim of the BEEHIVE project is to generate novel insight into HIV biology, evolution and epidemiology, leveraging next-generation high-throughput sequencing and bioinformatics to produce and analyse whole-genomes of viruses from approximately 3,000 European HIV-1 infected patients. These patients have known dates of infection spread over the last 25 years, good clinical follow up, and a wide range of clinical prognostic indicators and outcomes. The primary objective is to discover the viral genetic determinants of severity of infection and set-point viral load. This primary objective is high-risk & blue-skies: there is ample indirect evidence of polymorphisms that alter virulence, but they have never been identified, and it is not known how easy they are to discover. However, the project is also high-reward: it could lead to a substantial shift in the understanding of HIV disease.
Technologically, the BEEHIVE project will deliver new approaches for undertaking whole genome association studies on RNA viruses, including delivering an innovative high-throughput bioinformatics pipeline for handling genetically diverse viral quasi-species data (with viral diversity both within and between infected patients).
The project also includes secondary and tertiary objectives that address critical open questions in HIV epidemiology and evolution. The secondary objective is to use viral genetic sequences allied to mathematical epidemic models to better understand the resurgent European epidemic amongst high-risk groups, especially men who have sex with men. The aim will not just be to establish who is at risk of infection, which is known from conventional epidemiological approaches, but also to characterise the risk factors for onwards transmission of the virus. Tertiary objectives involve understanding the relationship between the genetic diversity within viral samples, indicative of on-going evolution or dual infections, to clinical outcomes.
Summary
The aim of the BEEHIVE project is to generate novel insight into HIV biology, evolution and epidemiology, leveraging next-generation high-throughput sequencing and bioinformatics to produce and analyse whole-genomes of viruses from approximately 3,000 European HIV-1 infected patients. These patients have known dates of infection spread over the last 25 years, good clinical follow up, and a wide range of clinical prognostic indicators and outcomes. The primary objective is to discover the viral genetic determinants of severity of infection and set-point viral load. This primary objective is high-risk & blue-skies: there is ample indirect evidence of polymorphisms that alter virulence, but they have never been identified, and it is not known how easy they are to discover. However, the project is also high-reward: it could lead to a substantial shift in the understanding of HIV disease.
Technologically, the BEEHIVE project will deliver new approaches for undertaking whole genome association studies on RNA viruses, including delivering an innovative high-throughput bioinformatics pipeline for handling genetically diverse viral quasi-species data (with viral diversity both within and between infected patients).
The project also includes secondary and tertiary objectives that address critical open questions in HIV epidemiology and evolution. The secondary objective is to use viral genetic sequences allied to mathematical epidemic models to better understand the resurgent European epidemic amongst high-risk groups, especially men who have sex with men. The aim will not just be to establish who is at risk of infection, which is known from conventional epidemiological approaches, but also to characterise the risk factors for onwards transmission of the virus. Tertiary objectives involve understanding the relationship between the genetic diversity within viral samples, indicative of on-going evolution or dual infections, to clinical outcomes.
Max ERC Funding
2 499 739 €
Duration
Start date: 2014-04-01, End date: 2019-03-31
Project acronym BIOSYNCEN
Project Dissection of centromeric chromatin and components: A biosynthetic approach
Researcher (PI) Patrick Heun
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary The centromere is one of the most important chromosomal elements. It is required for proper chromosome segregation in mitosis and meiosis and readily recognizable as the primary constriction of mitotic chromosomes. Proper centromere function is essential to ensure genome stability; therefore understanding centromere identity is directly relevant to cancer biology and gene therapy. How centromeres are established and maintained is however still an open question in the field. In most organisms this appears to be regulated by an epigenetic mechanism. The key candidate for such an epigenetic mark is CENH3 (CENP-A in mammals, CID in Drosophila), a centromere-specific histone H3 variant that is essential for centromere function and exclusively found in the nucleosomes of centromeric chromatin. Using a biosynthetic approach of force-targeting CENH3 in Drosophila to non-centromeric DNA, we were able to induce centromere function and demonstrate that CENH3 is sufficient to determine centromere identity. Here we propose to move this experimental setup across evolutionary boundaries into human cells to develop improved human artificial chromosomes (HACs). We will make further use of this unique setup to dissect the function of targeted CENH3 both in Drosophila and human cells. Contributing centromeric components and histone modifications of centromeric chromatin will be characterized in detail by mass spectroscopy in Drosophila. Finally we are proposing to develop a technique that allows high-resolution mapping of proteins on repetitive DNA to help further characterizing known and novel centromere components. This will be achieved by combining two independently established techniques: DNA methylation and DNA fiber combing. This ambitious proposal will significantly advance our understanding of how centromeres are determined and help the development of improved HACs for therapeutic applications in the future.
Summary
The centromere is one of the most important chromosomal elements. It is required for proper chromosome segregation in mitosis and meiosis and readily recognizable as the primary constriction of mitotic chromosomes. Proper centromere function is essential to ensure genome stability; therefore understanding centromere identity is directly relevant to cancer biology and gene therapy. How centromeres are established and maintained is however still an open question in the field. In most organisms this appears to be regulated by an epigenetic mechanism. The key candidate for such an epigenetic mark is CENH3 (CENP-A in mammals, CID in Drosophila), a centromere-specific histone H3 variant that is essential for centromere function and exclusively found in the nucleosomes of centromeric chromatin. Using a biosynthetic approach of force-targeting CENH3 in Drosophila to non-centromeric DNA, we were able to induce centromere function and demonstrate that CENH3 is sufficient to determine centromere identity. Here we propose to move this experimental setup across evolutionary boundaries into human cells to develop improved human artificial chromosomes (HACs). We will make further use of this unique setup to dissect the function of targeted CENH3 both in Drosophila and human cells. Contributing centromeric components and histone modifications of centromeric chromatin will be characterized in detail by mass spectroscopy in Drosophila. Finally we are proposing to develop a technique that allows high-resolution mapping of proteins on repetitive DNA to help further characterizing known and novel centromere components. This will be achieved by combining two independently established techniques: DNA methylation and DNA fiber combing. This ambitious proposal will significantly advance our understanding of how centromeres are determined and help the development of improved HACs for therapeutic applications in the future.
Max ERC Funding
1 755 960 €
Duration
Start date: 2013-02-01, End date: 2019-01-31
Project acronym CHROMATINRNA
Project The role of CpG island RNAs and Polycomb-RNA interactions in developmental gene regulation
Researcher (PI) Richard Gareth Jenner
Host Institution (HI) UNIVERSITY COLLEGE LONDON
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary A great challenge in developmental biology research has been to understand how cell type specific expression programs are orchestrated through regulated access to chromatin. The interaction between non-coding RNAs and chromatin regulators is emerging as an exciting new research area with the potential to explain how chromatin modifications are targeted.
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain developmental regulator genes specific for other cell types in a repressed state and is essential for embryogenesis across Metazoa. We have recently determined that CpG islands targeted by PRC2 generate a class of short non-coding RNAs. The RNAs are produced independently from mRNA, indicative of hitherto uncharacterised transcriptional processes. Furthermore, we have found that the PRC2 subunit Suz12 is an RNA binding protein and directly interacts with these short RNAs and with other RNAs in cells. The role of ncRNA in targeting PRC2 to CpG islands and the importance of PRC2 RNA binding activity for development remains to be understood. Our aims are to:
1. Determine the functional properties of CpG-island RNAs by A. identifying their conserved features, B. determining their role in polycomb targeting of CpG islands and C. investigating whether such a role relates to the antagonism of polycomb targeting by DNA methylation.
2. Establish the biological role for Suz12 RNA binding activity by A. determining the structural determinants for Suz12 binding in vitro, B. verifying these features play a role in PRC2 RNA binding in cells and C. determining the role for PRC2-RNA interactions for polycomb function and development.
This work promises to characterise a potentially fundamental aspect of cell biology and will open a number of avenues for understanding the function of ncRNAs, the RNA binding activity of chromatin regulators, how transcription and chromatin structure are regulated, and how cell state is maintained and reshaped during development.
Summary
A great challenge in developmental biology research has been to understand how cell type specific expression programs are orchestrated through regulated access to chromatin. The interaction between non-coding RNAs and chromatin regulators is emerging as an exciting new research area with the potential to explain how chromatin modifications are targeted.
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain developmental regulator genes specific for other cell types in a repressed state and is essential for embryogenesis across Metazoa. We have recently determined that CpG islands targeted by PRC2 generate a class of short non-coding RNAs. The RNAs are produced independently from mRNA, indicative of hitherto uncharacterised transcriptional processes. Furthermore, we have found that the PRC2 subunit Suz12 is an RNA binding protein and directly interacts with these short RNAs and with other RNAs in cells. The role of ncRNA in targeting PRC2 to CpG islands and the importance of PRC2 RNA binding activity for development remains to be understood. Our aims are to:
1. Determine the functional properties of CpG-island RNAs by A. identifying their conserved features, B. determining their role in polycomb targeting of CpG islands and C. investigating whether such a role relates to the antagonism of polycomb targeting by DNA methylation.
2. Establish the biological role for Suz12 RNA binding activity by A. determining the structural determinants for Suz12 binding in vitro, B. verifying these features play a role in PRC2 RNA binding in cells and C. determining the role for PRC2-RNA interactions for polycomb function and development.
This work promises to characterise a potentially fundamental aspect of cell biology and will open a number of avenues for understanding the function of ncRNAs, the RNA binding activity of chromatin regulators, how transcription and chromatin structure are regulated, and how cell state is maintained and reshaped during development.
Max ERC Funding
1 499 094 €
Duration
Start date: 2013-09-01, End date: 2019-04-30
Project acronym CONSERVREGCIRCUITRY
Project Conservation and Divergence of Tissue-Specific Transcriptional Regulation
Researcher (PI) Duncan Odom
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Vertebrates contain hundreds of different cell types which maintain phenotypic identity by a combination of epigenetic programming and genomic regulation. Systems biology approaches are now used in a number of laboratories to determine how transcription factors and chromatin marks pattern the human genome. Despite high conservation of the cellular and molecular function of many mammalian transcription factors, our recent experiments in matched mouse and human tissues indicates that most transcription factor binding events to DNA are very poorly conserved. A hypothesis that could account for this apparent divergence is that the larger regional pattern of transcription factor binding may be conserved. To test this, (1) we are characterizing the global transcriptional profile, chromatin state, and complete genomic occupancy of a set of tissue-specific transcription factors in hepatocytes of strategically chosen mammals; (2) to further identify the precise mechanistic contribution of cis and trans effects, we are comparing transcription factor binding at homologous regions of human and mouse DNA in a mouse line that carries human chromosome 21. Together, these projects will provide insight into the general principles of how transcriptional networks are evolutionarily conserved to regulate cell fate specification and function using a clinically important cell type as a model.
Summary
Vertebrates contain hundreds of different cell types which maintain phenotypic identity by a combination of epigenetic programming and genomic regulation. Systems biology approaches are now used in a number of laboratories to determine how transcription factors and chromatin marks pattern the human genome. Despite high conservation of the cellular and molecular function of many mammalian transcription factors, our recent experiments in matched mouse and human tissues indicates that most transcription factor binding events to DNA are very poorly conserved. A hypothesis that could account for this apparent divergence is that the larger regional pattern of transcription factor binding may be conserved. To test this, (1) we are characterizing the global transcriptional profile, chromatin state, and complete genomic occupancy of a set of tissue-specific transcription factors in hepatocytes of strategically chosen mammals; (2) to further identify the precise mechanistic contribution of cis and trans effects, we are comparing transcription factor binding at homologous regions of human and mouse DNA in a mouse line that carries human chromosome 21. Together, these projects will provide insight into the general principles of how transcriptional networks are evolutionarily conserved to regulate cell fate specification and function using a clinically important cell type as a model.
Max ERC Funding
960 000 €
Duration
Start date: 2008-10-01, End date: 2013-09-30
Project acronym Coupled gene circuit
Project Dynamics, noise, and coupling in gene circuit modules
Researcher (PI) James Charles Wallace Locke
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Starting Grant (StG), LS2, ERC-2013-StG
Summary Cells must integrate output from multiple genetic circuits in order to correctly control cellular processes. Despite much work characterizing regulation in these circuits, how circuits interact to control global cellular programs remains unclear. This is particularly true given that recent research at the single cell level has revealed that genetic circuits often generate variable or stochastic regulation dynamics. In this proposal we will use a multi-disciplinary approach, combining modelling and time-lapse microscopy, to investigate how cells can robustly integrate signals from multiple dynamic genetic circuits. In particular we will answer the following questions: 1) What types of dynamic signal encoding strategies are available for the cell? 2) What are the benefits of dynamic gene activation, whether stochastic or oscillatory, to the cell? 3) How do cells couple and integrate output from diverse gene modules despite the noise and variability observed in gene circuit dynamics?
We will study these questions using 2 key model systems. In Aim 1, we will examine stochastic pulse regulation dynamics and coupling between alternative sigma factors in B. subtilis. Our preliminary data has revealed that multiple B. subtilis sigma factors stochastically pulse under stress. We will look for evidence of any coupling or interactions between these stochastic pulse circuits. This system will serve as a model for how a cell uses stochastic pulsing to control diverse cellular processes. In Aim 2, we will examine coupling between a deterministic oscillator, the circadian clock, and multiple other key pathways in Cyanobacteria. We will examine how the cell can dynamically couple multiple cellular processes using an oscillating signal. This work will provide an excellent base for Aim 3, in which we will use synthetic biology approaches to develop ‘bottom up’ tests of generation of novel dynamic coupling strategies.
Summary
Cells must integrate output from multiple genetic circuits in order to correctly control cellular processes. Despite much work characterizing regulation in these circuits, how circuits interact to control global cellular programs remains unclear. This is particularly true given that recent research at the single cell level has revealed that genetic circuits often generate variable or stochastic regulation dynamics. In this proposal we will use a multi-disciplinary approach, combining modelling and time-lapse microscopy, to investigate how cells can robustly integrate signals from multiple dynamic genetic circuits. In particular we will answer the following questions: 1) What types of dynamic signal encoding strategies are available for the cell? 2) What are the benefits of dynamic gene activation, whether stochastic or oscillatory, to the cell? 3) How do cells couple and integrate output from diverse gene modules despite the noise and variability observed in gene circuit dynamics?
We will study these questions using 2 key model systems. In Aim 1, we will examine stochastic pulse regulation dynamics and coupling between alternative sigma factors in B. subtilis. Our preliminary data has revealed that multiple B. subtilis sigma factors stochastically pulse under stress. We will look for evidence of any coupling or interactions between these stochastic pulse circuits. This system will serve as a model for how a cell uses stochastic pulsing to control diverse cellular processes. In Aim 2, we will examine coupling between a deterministic oscillator, the circadian clock, and multiple other key pathways in Cyanobacteria. We will examine how the cell can dynamically couple multiple cellular processes using an oscillating signal. This work will provide an excellent base for Aim 3, in which we will use synthetic biology approaches to develop ‘bottom up’ tests of generation of novel dynamic coupling strategies.
Max ERC Funding
1 499 571 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym DARCGENS
Project Derived and Ancestral RNAs: Comparative Genomics and Evolution of ncRNAs
Researcher (PI) Christopher Paul Ponting
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary Much light has been shed on the number, mechanisms and functions of protein-coding genes in the human genome. In comparison, we know almost nothing about the origins and mechanisms of the functional dark matter , including sequence that is transcribed outside of protein-coding gene loci. This interdisciplinary proposal will capitalize on new theoretical and experimental opportunities to establish the extent by which long non-coding RNAs contribute to mammalian and fruit fly biology. Since 2001, the Ponting group has pioneered the comparative analysis of protein-coding genes across the amniotes and Drosophilids within many international genome sequencing consortia. This Advanced Grant will break new ground by applying these approaches to long intergenic non-coding RNA (lincRNA) genes from mammals to birds and to flies. The Grant will allow Ponting to free himself of the constraints normally associated with in silico analyses by analysing lincRNAs in vitro and in vivo. The integration of computational and experimental approaches for lincRNAs from across the metazoan tree provides a powerful new toolkit for elucidating the origins and biological roles of these enigmatic molecules. Catalogues of lincRNA loci will be built for human, mouse, fruit fly, zebrafinch, chicken and Aplysia by exploiting data from next-generation sequencing technologies. This will immediately provide a new perspective on how these loci arise, evolve and function, including whether their orthologues are apparent across diverse species. Using new evidence that lincRNA loci act in cis with neighbouring protein-coding loci, we will determine lincRNA mechanisms and will establish the consequences of lincRNA knock-down, knock-out and over-expression in mouse, chick and fruitfly.
Summary
Much light has been shed on the number, mechanisms and functions of protein-coding genes in the human genome. In comparison, we know almost nothing about the origins and mechanisms of the functional dark matter , including sequence that is transcribed outside of protein-coding gene loci. This interdisciplinary proposal will capitalize on new theoretical and experimental opportunities to establish the extent by which long non-coding RNAs contribute to mammalian and fruit fly biology. Since 2001, the Ponting group has pioneered the comparative analysis of protein-coding genes across the amniotes and Drosophilids within many international genome sequencing consortia. This Advanced Grant will break new ground by applying these approaches to long intergenic non-coding RNA (lincRNA) genes from mammals to birds and to flies. The Grant will allow Ponting to free himself of the constraints normally associated with in silico analyses by analysing lincRNAs in vitro and in vivo. The integration of computational and experimental approaches for lincRNAs from across the metazoan tree provides a powerful new toolkit for elucidating the origins and biological roles of these enigmatic molecules. Catalogues of lincRNA loci will be built for human, mouse, fruit fly, zebrafinch, chicken and Aplysia by exploiting data from next-generation sequencing technologies. This will immediately provide a new perspective on how these loci arise, evolve and function, including whether their orthologues are apparent across diverse species. Using new evidence that lincRNA loci act in cis with neighbouring protein-coding loci, we will determine lincRNA mechanisms and will establish the consequences of lincRNA knock-down, knock-out and over-expression in mouse, chick and fruitfly.
Max ERC Funding
2 400 000 €
Duration
Start date: 2010-05-01, End date: 2015-04-30
Project acronym DEVOCHROMO
Project Chromosome structure and genome organization in early mammalian development
Researcher (PI) Peter Fraser
Host Institution (HI) THE BABRAHAM INSTITUTE
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary "The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Summary
"The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Max ERC Funding
2 401 393 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym dynamicmodifications
Project Complexity and dynamics of nucleic acids modifications in vivo
Researcher (PI) Petra Hajkova
Host Institution (HI) IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
Call Details Consolidator Grant (CoG), LS2, ERC-2014-CoG
Summary Development of any organism starts with a totipotent cell (zygote). Through series of cell divisions and differentiation processes this cell will eventually give rise to the whole organism containing hundreds of specialised cell. While the cells at the onset of development have the capacity to generate all cell types (ie are toti-or pluripotent), this developmental capacity is progressively lost as the cells undertake cell fate decisions. At the molecular level, the memory of these events is laid down in a complex layer of epigenetic modifications at both the DNA and the chromatin level. Unidirectional character of the developmental progress dictates that the key acquired epigenetic modifications are stable and inherited through subsequent cell divisions. This paradigm is, however, challenged during cellular reprogramming that requires de-differentiation (nuclear transfer, induced pluripotent stem cells, wound healing and regeneration in lower organisms) or a change in cell fate (transdifferentiation). Despite intense efforts of numerous research teams, the molecular mechanisms of these processes remain enigmatic.
In order to understand cellular reprogramming at the molecular level, this proposal takes advantage of epigenetic reprogramming processes that occur naturally during mouse development. By using mouse fertilised zygote and mouse developing primordial germ cells we will investigate novel molecular components implicated in the genome-wide erasure of DNA methylation. Additionally, by using a unique combination of the developmental models with the state of the art ultra-sensitive LC/MS and genomics approaches we propose to investigate the dynamics and the interplay between DNA and RNA modifications during these key periods of embryonic development characterised by genome-wide epigenetic changes . Our work will thus provide new fundamental insights into a complex dynamics and interactions between epigenetic modifications that underlie epigenetic reprogramming
Summary
Development of any organism starts with a totipotent cell (zygote). Through series of cell divisions and differentiation processes this cell will eventually give rise to the whole organism containing hundreds of specialised cell. While the cells at the onset of development have the capacity to generate all cell types (ie are toti-or pluripotent), this developmental capacity is progressively lost as the cells undertake cell fate decisions. At the molecular level, the memory of these events is laid down in a complex layer of epigenetic modifications at both the DNA and the chromatin level. Unidirectional character of the developmental progress dictates that the key acquired epigenetic modifications are stable and inherited through subsequent cell divisions. This paradigm is, however, challenged during cellular reprogramming that requires de-differentiation (nuclear transfer, induced pluripotent stem cells, wound healing and regeneration in lower organisms) or a change in cell fate (transdifferentiation). Despite intense efforts of numerous research teams, the molecular mechanisms of these processes remain enigmatic.
In order to understand cellular reprogramming at the molecular level, this proposal takes advantage of epigenetic reprogramming processes that occur naturally during mouse development. By using mouse fertilised zygote and mouse developing primordial germ cells we will investigate novel molecular components implicated in the genome-wide erasure of DNA methylation. Additionally, by using a unique combination of the developmental models with the state of the art ultra-sensitive LC/MS and genomics approaches we propose to investigate the dynamics and the interplay between DNA and RNA modifications during these key periods of embryonic development characterised by genome-wide epigenetic changes . Our work will thus provide new fundamental insights into a complex dynamics and interactions between epigenetic modifications that underlie epigenetic reprogramming
Max ERC Funding
2 000 000 €
Duration
Start date: 2015-08-01, End date: 2020-07-31
Project acronym ELABORATE
Project Elucidation of the molecular and functional basis of disease phenotypes in the rat model
Researcher (PI) Timothy Aitman
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Advanced Grant (AdG), LS2, ERC-2010-AdG_20100317
Summary Recent genetic studies have identified hundreds of susceptibility genes for common human diseases but genetic effects are small and identifying underlying mechanisms remains challenging. Rodent models offer significant advantages for analysis of disease phenotypes. Advances in genome resources and gene targeting have increased the attractiveness of the rat model for genetic studies but progress has been hampered by absence of relevant rat genome sequences.
We recently sequenced the genome of the spontaneously hypertensive rat (SHR) and will shortly have completed the Wistar Kyoto (WKY) rat sequence. The SHR genome contains over 750 genes that are completely or partly deleted, or have a frameshift in their open reading frame. These sequence variants, along with variants controlling dysregulated gene expression that we characterised previously, most likely include the major determinants of SHR cardiovascular and metabolic disease phenotypes.
We shall determine the functional consequences of these variants by creating and phenotyping transgenic and knockout rats on the SHR and WKY genetic backgrounds, using transposon-mediated transgenesis and zinc-finger nuclease-mediated gene deletion recently shown to be highly efficient in rats. Genes will be prioritised for study by statistical and informatic analyses using our extensive physiological, gene expression and linkage data in these rat strains, and by comparative analysis with data from human genome-wide association studies. Confirmed rat disease genes will be tested for conserved functions in humans.
These proposals provide a systematic route to elucidating the molecular and functional basis of disease phenotypes in SHR and WKY rats, and for translating these findings to advance understanding of common human diseases.
Summary
Recent genetic studies have identified hundreds of susceptibility genes for common human diseases but genetic effects are small and identifying underlying mechanisms remains challenging. Rodent models offer significant advantages for analysis of disease phenotypes. Advances in genome resources and gene targeting have increased the attractiveness of the rat model for genetic studies but progress has been hampered by absence of relevant rat genome sequences.
We recently sequenced the genome of the spontaneously hypertensive rat (SHR) and will shortly have completed the Wistar Kyoto (WKY) rat sequence. The SHR genome contains over 750 genes that are completely or partly deleted, or have a frameshift in their open reading frame. These sequence variants, along with variants controlling dysregulated gene expression that we characterised previously, most likely include the major determinants of SHR cardiovascular and metabolic disease phenotypes.
We shall determine the functional consequences of these variants by creating and phenotyping transgenic and knockout rats on the SHR and WKY genetic backgrounds, using transposon-mediated transgenesis and zinc-finger nuclease-mediated gene deletion recently shown to be highly efficient in rats. Genes will be prioritised for study by statistical and informatic analyses using our extensive physiological, gene expression and linkage data in these rat strains, and by comparative analysis with data from human genome-wide association studies. Confirmed rat disease genes will be tested for conserved functions in humans.
These proposals provide a systematic route to elucidating the molecular and functional basis of disease phenotypes in SHR and WKY rats, and for translating these findings to advance understanding of common human diseases.
Max ERC Funding
2 476 108 €
Duration
Start date: 2011-06-01, End date: 2017-05-31
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
