Project acronym ACTIVATION OF XCI
Project Molecular mechanisms controlling X chromosome inactivation
Researcher (PI) Joost Henk Gribnau
Host Institution (HI) ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary In mammals, gene dosage of X-chromosomal genes is equalized between sexes by random inactivation of either one of the two X chromosomes in female cells. In the initial phase of X chromosome inactivation (XCI), a counting and initiation process determines the number of X chromosomes per nucleus, and elects the future inactive X chromosome (Xi). Xist is an X-encoded gene that plays a crucial role in the XCI process. At the start of XCI Xist expression is up-regulated and Xist RNA accumulates on the future Xi thereby initiating silencing in cis. Recent work performed in my laboratory indicates that the counting and initiation process is directed by a stochastic mechanism, in which each X chromosome has an independent probability to be inactivated. We also found that this probability is determined by the X:ploïdy ratio. These results indicated the presence of at least one X-linked activator of XCI. With a BAC screen we recently identified X-encoded RNF12 to be a dose-dependent activator of XCI. Expression of RNF12 correlates with Xist expression, and a heterozygous deletion of Rnf12 results in a marked loss of XCI in female cells. The presence of a small proportion of cells that still initiate XCI, in Rnf12+/- cells, also indicated that more XCI-activators are involved in XCI. Here, we propose to investigate the molecular mechanism by which RNF12 activates XCI in mouse and human, and to search for additional XCI-activators. We will also attempt to establish the role of different inhibitors of XCI, including CTCF and the pluripotency factors OCT4, SOX2 and NANOG. We anticipate that these studies will significantly advance our understanding of XCI mechanisms, which is highly relevant for a better insight in the manifestation of X-linked diseases that are affected by XCI.
Summary
In mammals, gene dosage of X-chromosomal genes is equalized between sexes by random inactivation of either one of the two X chromosomes in female cells. In the initial phase of X chromosome inactivation (XCI), a counting and initiation process determines the number of X chromosomes per nucleus, and elects the future inactive X chromosome (Xi). Xist is an X-encoded gene that plays a crucial role in the XCI process. At the start of XCI Xist expression is up-regulated and Xist RNA accumulates on the future Xi thereby initiating silencing in cis. Recent work performed in my laboratory indicates that the counting and initiation process is directed by a stochastic mechanism, in which each X chromosome has an independent probability to be inactivated. We also found that this probability is determined by the X:ploïdy ratio. These results indicated the presence of at least one X-linked activator of XCI. With a BAC screen we recently identified X-encoded RNF12 to be a dose-dependent activator of XCI. Expression of RNF12 correlates with Xist expression, and a heterozygous deletion of Rnf12 results in a marked loss of XCI in female cells. The presence of a small proportion of cells that still initiate XCI, in Rnf12+/- cells, also indicated that more XCI-activators are involved in XCI. Here, we propose to investigate the molecular mechanism by which RNF12 activates XCI in mouse and human, and to search for additional XCI-activators. We will also attempt to establish the role of different inhibitors of XCI, including CTCF and the pluripotency factors OCT4, SOX2 and NANOG. We anticipate that these studies will significantly advance our understanding of XCI mechanisms, which is highly relevant for a better insight in the manifestation of X-linked diseases that are affected by XCI.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym CHROMATINPRINCIPLES
Project Principles of Chromatin Organization
Researcher (PI) Bas Van Steensel
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary Chromatin is the ensemble of genomic DNA and hundreds of structural and regulatory proteins. Together these proteins govern the gene expression program of a cell. While biochemical and genetic approaches have tought us much about interactions between individual chromatin proteins, we still lack a “big picture” of chromatin: how is the entire interaction network of chromatin proteins organized?
My lab discovered that chromatin in Drosophila consists of a limited number of principal types that partition the genome into domains with distinct regulatory properties. Among these is BLACK chromatin, a novel repressive type of chromatin that covers nearly half of the fly genome. It is still largely unclear how these different chromatin types are formed, how they are targeted to specific genomic regions, and how they interact with each other.
Here, I propose a combination of systematic approaches aimed to gain insight into the basic mechanisms that drive the partioning of the genome into distinct chromatin types. New genomics techniques, developed in my laboratory, will be used to construct an integrated view of the interplay of more than one hundred representative chromatin proteins with each other and with sequence elements in the genome. Specifically, we will: (1) Study the genome-wide dynamic repositioning of chromatin domains during development in relation to gene regulation; (2) Use a novel and versatile parallel genome-wide reporter assay to dissect the interplay among DNA sequences and chromatin types; (3) Combine computational modeling with a high-throughput genome-wide assay to uncover the network of interactions responsible for the formation of the principal chromatin types; (4) Dissect the molecular architecture of BLACK chromatin and its role in gene repression.
The results will provide understanding of the basic principles that govern the structure and composition of chromatin, and reveal how the principal chromatin types together direct gene expression.
Summary
Chromatin is the ensemble of genomic DNA and hundreds of structural and regulatory proteins. Together these proteins govern the gene expression program of a cell. While biochemical and genetic approaches have tought us much about interactions between individual chromatin proteins, we still lack a “big picture” of chromatin: how is the entire interaction network of chromatin proteins organized?
My lab discovered that chromatin in Drosophila consists of a limited number of principal types that partition the genome into domains with distinct regulatory properties. Among these is BLACK chromatin, a novel repressive type of chromatin that covers nearly half of the fly genome. It is still largely unclear how these different chromatin types are formed, how they are targeted to specific genomic regions, and how they interact with each other.
Here, I propose a combination of systematic approaches aimed to gain insight into the basic mechanisms that drive the partioning of the genome into distinct chromatin types. New genomics techniques, developed in my laboratory, will be used to construct an integrated view of the interplay of more than one hundred representative chromatin proteins with each other and with sequence elements in the genome. Specifically, we will: (1) Study the genome-wide dynamic repositioning of chromatin domains during development in relation to gene regulation; (2) Use a novel and versatile parallel genome-wide reporter assay to dissect the interplay among DNA sequences and chromatin types; (3) Combine computational modeling with a high-throughput genome-wide assay to uncover the network of interactions responsible for the formation of the principal chromatin types; (4) Dissect the molecular architecture of BLACK chromatin and its role in gene repression.
The results will provide understanding of the basic principles that govern the structure and composition of chromatin, and reveal how the principal chromatin types together direct gene expression.
Max ERC Funding
2 495 080 €
Duration
Start date: 2012-03-01, End date: 2017-02-28
Project acronym DENOVO
Project Detection and interpretation of de novo mutations and structural genomic variations in mental retardation
Researcher (PI) Joris Andre Veltman
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Mental retardation, like most common neurodevelopmental and psychiatric diseases, shows a strong genetic component, but these underlying genetic causes remain largely unknown. For a long time it was hypothesized that these kind of common diseases are mainly caused by common inherited genetic variants with reduced penetrance. In contrast to this common variant-common disease hypothesis, I here hypothesize that a large proportion of this so-called “missing heritability” for conditions such as mental retardation, schizophrenia, and autism lies in de novo genetic variation that is rapidly eliminated from the population because individuals with such diseases have severely compromised fecundity.
My previous work using microarrays has already demonstrated de novo genomic copy number variations in mental retardation and in schizophrenia. However, microarrays do not allow us to capture the most common form of de novo mutations, those occurring at the nucleotide level. Technological innovations now for the first time allow us to comprehensively study the entire genome of an individual for genomic variations at all levels. In this project I will explore the de novo mutation hypothesis in whole exome and whole genome sequence data from patients with mental retardation. I will optimize and apply whole genome sequencing strategies using patient-parent trios, both in rare mental retardation syndromes as well as common forms of mental retardation. Guidelines for pathogenicity will be established by computational studies aimed at unraveling genotype-phenotype correlations in these family-based genome sequence type datasets.
This project will contribute significantly to resolving the genetic causes of reproductively lethal disorders such as mental retardation, provide critical knowledge on the frequency and consequences of de novo mutations in our genome and help to establish medical genome sequencing as a routine diagnostic approach.
Summary
Mental retardation, like most common neurodevelopmental and psychiatric diseases, shows a strong genetic component, but these underlying genetic causes remain largely unknown. For a long time it was hypothesized that these kind of common diseases are mainly caused by common inherited genetic variants with reduced penetrance. In contrast to this common variant-common disease hypothesis, I here hypothesize that a large proportion of this so-called “missing heritability” for conditions such as mental retardation, schizophrenia, and autism lies in de novo genetic variation that is rapidly eliminated from the population because individuals with such diseases have severely compromised fecundity.
My previous work using microarrays has already demonstrated de novo genomic copy number variations in mental retardation and in schizophrenia. However, microarrays do not allow us to capture the most common form of de novo mutations, those occurring at the nucleotide level. Technological innovations now for the first time allow us to comprehensively study the entire genome of an individual for genomic variations at all levels. In this project I will explore the de novo mutation hypothesis in whole exome and whole genome sequence data from patients with mental retardation. I will optimize and apply whole genome sequencing strategies using patient-parent trios, both in rare mental retardation syndromes as well as common forms of mental retardation. Guidelines for pathogenicity will be established by computational studies aimed at unraveling genotype-phenotype correlations in these family-based genome sequence type datasets.
This project will contribute significantly to resolving the genetic causes of reproductively lethal disorders such as mental retardation, provide critical knowledge on the frequency and consequences of de novo mutations in our genome and help to establish medical genome sequencing as a routine diagnostic approach.
Max ERC Funding
1 499 154 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym DIATOMITE
Project Genome-enabled dissection of marine diatom ecophysiology
Researcher (PI) Chris Bowler
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary "Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean. Recently completed whole genome sequences have revealed a wealth of information about the evolutionary origins and metabolic adaptations that may have led to their ecological success. A major finding is that they have acquired genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel and largely unexplored capacities for metabolic management. The project will address the current gap in knowledge about the physiological functions of diatom gene products and about the evolutionary mechanisms that have led to diatom success in contemporary oceans. We will exploit genome-enabled approaches to pioneer new research topics addressing:
1. How has diatom evolution enabled interactions between chloroplasts and mitochondria that have provided diatoms with physiological and metabolic innovations?
2. What are the relative contributions of DNA sequence variation and epigenetic processes in diatom adaptive dynamics?
By combining these questions, we will uniquely be able to identify sentinel genes that have driven major physiological and metabolic innovations in diatoms, and will explore the mechanisms that have selected and molded them during diatom evolution. We will focus our studies largely on diatom responses to nutrients, in particular nitrate and iron, and will exploit the advantages of Phaeodactylum tricornutum as a model diatom species for reverse genetics. The proposed studies will revisit textbook understanding of photosynthesis and nitrogen metabolism, and will refine hypotheses about why diatoms dominate in contemporary ocean settings. By placing our studies in evolutionary and ecological contexts, in particular by examining the contribution of epigenetic processes in diatoms, our work will furthermore provide insights into how the environment selects for fitness in phytoplankton."
Summary
"Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean. Recently completed whole genome sequences have revealed a wealth of information about the evolutionary origins and metabolic adaptations that may have led to their ecological success. A major finding is that they have acquired genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel and largely unexplored capacities for metabolic management. The project will address the current gap in knowledge about the physiological functions of diatom gene products and about the evolutionary mechanisms that have led to diatom success in contemporary oceans. We will exploit genome-enabled approaches to pioneer new research topics addressing:
1. How has diatom evolution enabled interactions between chloroplasts and mitochondria that have provided diatoms with physiological and metabolic innovations?
2. What are the relative contributions of DNA sequence variation and epigenetic processes in diatom adaptive dynamics?
By combining these questions, we will uniquely be able to identify sentinel genes that have driven major physiological and metabolic innovations in diatoms, and will explore the mechanisms that have selected and molded them during diatom evolution. We will focus our studies largely on diatom responses to nutrients, in particular nitrate and iron, and will exploit the advantages of Phaeodactylum tricornutum as a model diatom species for reverse genetics. The proposed studies will revisit textbook understanding of photosynthesis and nitrogen metabolism, and will refine hypotheses about why diatoms dominate in contemporary ocean settings. By placing our studies in evolutionary and ecological contexts, in particular by examining the contribution of epigenetic processes in diatoms, our work will furthermore provide insights into how the environment selects for fitness in phytoplankton."
Max ERC Funding
2 423 320 €
Duration
Start date: 2012-06-01, End date: 2017-05-31
Project acronym DICIG
Project Dynamic Interplay between Eukaryotic Chromosomes: Impact on Genome Stability
Researcher (PI) Romain Nicolas André Koszul
Host Institution (HI) INSTITUT PASTEUR
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary The structure and role of the DNA molecule raise fascinating questions regarding its dynamics, i.e. not only the tri-dimensional reorganisation associated with functional events at short time-scale, but also the structural changes, i.e. rearrangements, that occur in the chromosome over generations. It is increasingly obvious that the physical properties of both the chromosomes and their environment the nucleoplasm, the nuclear periphery, cytoskeleton, etc. are playing important roles in the dynamic changes observed. For instance, we recently showed that chromosome movements during mid-prophase of meiosis in budding yeast result from a trans-acting force generated at the level of the global cytoskeleton network, suggesting that extranuclear mechanical trans-acting signals could also regulate chromosomal metabolism in other ways. Our objectives are to make important contributions to the understanding of the mechanical and functional interplay between the cytoskeleton, the nuclear periphery, and chromosomes through in vitro and in vivo interdisciplinary approaches. We will investigate three questions of fundamental importance: i) the potential transmission and function of mechanical forces from the cytoskeleton to chromatin during interphase, ii) the physical principles that govern chromosome reorganization under mechanical force in vitro, and iii) the global chromatin dynamics during the fundamental S phase and its impact on genome stability. We will use a combination of high-resolution imaging, micromanipulation, and high-throughput molecular techniques (chromosome conformation capture and ChIP-Seq) to reach our goals. Most of these studies will be performed in budding yeast, but will have repercussions in our understanding of higher eukaryotes metabolism.
Summary
The structure and role of the DNA molecule raise fascinating questions regarding its dynamics, i.e. not only the tri-dimensional reorganisation associated with functional events at short time-scale, but also the structural changes, i.e. rearrangements, that occur in the chromosome over generations. It is increasingly obvious that the physical properties of both the chromosomes and their environment the nucleoplasm, the nuclear periphery, cytoskeleton, etc. are playing important roles in the dynamic changes observed. For instance, we recently showed that chromosome movements during mid-prophase of meiosis in budding yeast result from a trans-acting force generated at the level of the global cytoskeleton network, suggesting that extranuclear mechanical trans-acting signals could also regulate chromosomal metabolism in other ways. Our objectives are to make important contributions to the understanding of the mechanical and functional interplay between the cytoskeleton, the nuclear periphery, and chromosomes through in vitro and in vivo interdisciplinary approaches. We will investigate three questions of fundamental importance: i) the potential transmission and function of mechanical forces from the cytoskeleton to chromatin during interphase, ii) the physical principles that govern chromosome reorganization under mechanical force in vitro, and iii) the global chromatin dynamics during the fundamental S phase and its impact on genome stability. We will use a combination of high-resolution imaging, micromanipulation, and high-throughput molecular techniques (chromosome conformation capture and ChIP-Seq) to reach our goals. Most of these studies will be performed in budding yeast, but will have repercussions in our understanding of higher eukaryotes metabolism.
Max ERC Funding
1 497 000 €
Duration
Start date: 2011-06-01, End date: 2017-05-31
Project acronym EVOIMMUNOPOP
Project Human Evolutionary Immunogenomics: population genetic variation in immune responses
Researcher (PI) Lluis Quintana-Murci
Host Institution (HI) INSTITUT PASTEUR
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Recent genome-wide association studies have successfully identified rare and common variants that correlate with complex traits. However, they have provided us with little insight into the nature of the genetic, biological and evolutionary relationships underlying such complex phenotypes. There is thus a growing need for approaches that provide a mechanistic understanding of how genetic variants function to impact phenotypic variation and why they have been substrates of natural selection. One set of traits that displays considerable heterogeneity and that has undoubtedly been shaped by natural selection is the host response to microorganisms. By integrating cutting-edge knowledge and technology in the fields of genomics, population genetics, immunology and bioinformatics, our aim is to establish a thorough understanding of how variable the human immune response is in the natural setting and how this phenotypic variation is under genetic control. Specifically, we aim (i) to characterise the genetic architecture of two populations differing in their ethnic background; (ii) to define individual and population-level variation in immune responses, in the same individuals, by establishing an ex vivo cell-based model to study levels of transcript abundance of both mRNA and miRNA, before and after activation with various immune stimuli; (iii) to map expression quantitative trait loci associated with variation in immune responses; and (iv) to identify adaptive immunological phenotypes. This study will increase our understanding of how genotypes influence the heterogeneity of immune response phenotypes at the level of the human population, and reveal immunological mechanisms under genetic control that have been crucial for our past and present survival against infection. In doing so, we will provide the foundations to define perturbations in these responses that correlate with the occurrence of various infectious and non-infectious diseases as well as with vaccine success.
Summary
Recent genome-wide association studies have successfully identified rare and common variants that correlate with complex traits. However, they have provided us with little insight into the nature of the genetic, biological and evolutionary relationships underlying such complex phenotypes. There is thus a growing need for approaches that provide a mechanistic understanding of how genetic variants function to impact phenotypic variation and why they have been substrates of natural selection. One set of traits that displays considerable heterogeneity and that has undoubtedly been shaped by natural selection is the host response to microorganisms. By integrating cutting-edge knowledge and technology in the fields of genomics, population genetics, immunology and bioinformatics, our aim is to establish a thorough understanding of how variable the human immune response is in the natural setting and how this phenotypic variation is under genetic control. Specifically, we aim (i) to characterise the genetic architecture of two populations differing in their ethnic background; (ii) to define individual and population-level variation in immune responses, in the same individuals, by establishing an ex vivo cell-based model to study levels of transcript abundance of both mRNA and miRNA, before and after activation with various immune stimuli; (iii) to map expression quantitative trait loci associated with variation in immune responses; and (iv) to identify adaptive immunological phenotypes. This study will increase our understanding of how genotypes influence the heterogeneity of immune response phenotypes at the level of the human population, and reveal immunological mechanisms under genetic control that have been crucial for our past and present survival against infection. In doing so, we will provide the foundations to define perturbations in these responses that correlate with the occurrence of various infectious and non-infectious diseases as well as with vaccine success.
Max ERC Funding
1 494 756 €
Duration
Start date: 2012-01-01, End date: 2017-08-31
Project acronym GENENOISECONTROL
Project Controlling stochastic gene expression during development and stem cell differentiation
Researcher (PI) Alexander Van Oudenaarden
Host Institution (HI) KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogenous environments vary, suggesting that randomness in developmental processes such as gene expression may also generate diversity. My laboratory has intensively studied stochastic gene expression in microbial systems and more recently started to apply these concepts to multicellular organisms and stem cells. One of the major lessons learned from our work and others is that microbial systems tend to exploit stochastic gene expression by introducing phenotypic diversity into the population. However it is an open question whether stochastic gene expression benefits or hinders decision-making by cells in a developing embryo. On the one hand, the gene expression patterns of different cells during metazoan development must be aligned either to ensure proper tissue formation or maintain a coordinated timing of developmental events. This suggests that stochastic fluctuations in gene expression may be controlled or their effects may be buffered under normal conditions. On the other hand, stem cells might use fluctuations to prime differentiation. A stem cell might continuously fluctuate between different primed states each biased towards a different germ layer fate. As soon as an external differentiation signal appears the cell would rapidly differentiate towards the fate that was stochastically selected. The overarching goal of this proposal is to the understand how stochastic gene expression is controlled, or utilized, during development and stem cell differentiation using the nematode worm Caenorhabditis elegans and murine embryonic stem cells as experimental model systems. To obtain this goal we will use a combination of quantitative experiments, theoretical and computational approaches, and the development of novel technology.
Summary
The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogenous environments vary, suggesting that randomness in developmental processes such as gene expression may also generate diversity. My laboratory has intensively studied stochastic gene expression in microbial systems and more recently started to apply these concepts to multicellular organisms and stem cells. One of the major lessons learned from our work and others is that microbial systems tend to exploit stochastic gene expression by introducing phenotypic diversity into the population. However it is an open question whether stochastic gene expression benefits or hinders decision-making by cells in a developing embryo. On the one hand, the gene expression patterns of different cells during metazoan development must be aligned either to ensure proper tissue formation or maintain a coordinated timing of developmental events. This suggests that stochastic fluctuations in gene expression may be controlled or their effects may be buffered under normal conditions. On the other hand, stem cells might use fluctuations to prime differentiation. A stem cell might continuously fluctuate between different primed states each biased towards a different germ layer fate. As soon as an external differentiation signal appears the cell would rapidly differentiate towards the fate that was stochastically selected. The overarching goal of this proposal is to the understand how stochastic gene expression is controlled, or utilized, during development and stem cell differentiation using the nematode worm Caenorhabditis elegans and murine embryonic stem cells as experimental model systems. To obtain this goal we will use a combination of quantitative experiments, theoretical and computational approaches, and the development of novel technology.
Max ERC Funding
2 500 000 €
Duration
Start date: 2012-04-01, End date: 2017-03-31
Project acronym GENTB
Project Human Genetics of Tuberculosis
Researcher (PI) Laurent - Marcel Abel
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Call Details Advanced Grant (AdG), LS2, ERC-2010-AdG_20100317
Summary Tuberculosis (TB) is not only an infectious disease, as only a small fraction of individuals infected with Mycobacterium tuberculosis (Mtb) develop disease. Over the last century, evidence has accumulated indicating that TB is also a genetic disease. However, the molecular basis of predisposition to TB remains elusive, and efforts to understand the pathogenesis of TB are of prime importance if we are to combat this major killer of mankind. The PI proposes an integrated and innovative research program aiming to identify the genetic variants controlling the critical steps of the process from exposure to Mtb to development of TB. In addition to investigating the two key clinical phenotypes - the development of disseminated TB in children and of pulmonary TB in adults - this program proposes to undertake the first comprehensive genetic dissection of resistance to Mtb infection. Making use of the latest conceptual and technical breakthroughs in human genetics, the strategy will combine Mendelian and complex genetics approaches, including genome-wide (GW) investigations (GW linkage and association studies, whole-exome sequencing). The strengths of this innovative, ground-breaking project lie in its bold hypothesis, the high quality of our clinical samples, and the extensive experience of our laboratory in human genetics of mycobacterial infections in terms of genetic epidemiology, molecular genetics, and immunology. The identification of the main variants controlling TB development will have major implications for TB control, both in the definition of new prevention strategies (design of vaccine research and clinical trials) and in the development of new treatments (aiming to restore deficient immune responses). These findings will also shift paradigms in both human genetics and infectious diseases, as - genetic TB - could provide proof-of-principle for a genetic theory of common infectious diseases.
Summary
Tuberculosis (TB) is not only an infectious disease, as only a small fraction of individuals infected with Mycobacterium tuberculosis (Mtb) develop disease. Over the last century, evidence has accumulated indicating that TB is also a genetic disease. However, the molecular basis of predisposition to TB remains elusive, and efforts to understand the pathogenesis of TB are of prime importance if we are to combat this major killer of mankind. The PI proposes an integrated and innovative research program aiming to identify the genetic variants controlling the critical steps of the process from exposure to Mtb to development of TB. In addition to investigating the two key clinical phenotypes - the development of disseminated TB in children and of pulmonary TB in adults - this program proposes to undertake the first comprehensive genetic dissection of resistance to Mtb infection. Making use of the latest conceptual and technical breakthroughs in human genetics, the strategy will combine Mendelian and complex genetics approaches, including genome-wide (GW) investigations (GW linkage and association studies, whole-exome sequencing). The strengths of this innovative, ground-breaking project lie in its bold hypothesis, the high quality of our clinical samples, and the extensive experience of our laboratory in human genetics of mycobacterial infections in terms of genetic epidemiology, molecular genetics, and immunology. The identification of the main variants controlling TB development will have major implications for TB control, both in the definition of new prevention strategies (design of vaccine research and clinical trials) and in the development of new treatments (aiming to restore deficient immune responses). These findings will also shift paradigms in both human genetics and infectious diseases, as - genetic TB - could provide proof-of-principle for a genetic theory of common infectious diseases.
Max ERC Funding
2 047 913 €
Duration
Start date: 2011-06-01, End date: 2016-05-31
Project acronym I2ST
Project Initiating and interfering with silencing of transposons
Researcher (PI) Olivier Mathieu
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary There is no living organism that does not contain transposons, and they make up a significant fraction, and in some instances, the vast majority of the genome in a given species. Owing to their proliferation propensity, these mobile genetic elements can create genetic variability providing selective benefits, but they also have a mutagenic potential. Therefore, host genomes have evolved epigenetic surveillance mechanisms to recognize and silence transposons. If maintenance of silencing is rather well understood, little is know about how the host recognize transposons as non-self elements and initiate silencing as they invade the genome. Also, although several examples indicate that a variety of environmental factors can reverse transposon silencing, how such factors interfere with the silencing machinery is largely unknown. The proposed research project will make use of our recent discovery of active endogenous retrotransposons in Arabidopsis to decipher genetically the mechanisms involved in initiating silencing of a transposon. In parallel, we will characterize how DNA-methylation associated silencing can be efficiently re-established once it has been lost, and use a genome-wide approach to determine the extent of this phenomenon. Finally, we intend to determine the genome-wide impact of a stress on transposon silencing and to genetically identify and characterize the molecular bases of stress-induced release of silencing at transposons. Our studies have the potential to bring general insights into how transposons have been so successful in colonizing host genomes, how they are kept under tight control and can be unleashed thereby contributing to genome plasticity and environmental adaptation.
Summary
There is no living organism that does not contain transposons, and they make up a significant fraction, and in some instances, the vast majority of the genome in a given species. Owing to their proliferation propensity, these mobile genetic elements can create genetic variability providing selective benefits, but they also have a mutagenic potential. Therefore, host genomes have evolved epigenetic surveillance mechanisms to recognize and silence transposons. If maintenance of silencing is rather well understood, little is know about how the host recognize transposons as non-self elements and initiate silencing as they invade the genome. Also, although several examples indicate that a variety of environmental factors can reverse transposon silencing, how such factors interfere with the silencing machinery is largely unknown. The proposed research project will make use of our recent discovery of active endogenous retrotransposons in Arabidopsis to decipher genetically the mechanisms involved in initiating silencing of a transposon. In parallel, we will characterize how DNA-methylation associated silencing can be efficiently re-established once it has been lost, and use a genome-wide approach to determine the extent of this phenomenon. Finally, we intend to determine the genome-wide impact of a stress on transposon silencing and to genetically identify and characterize the molecular bases of stress-induced release of silencing at transposons. Our studies have the potential to bring general insights into how transposons have been so successful in colonizing host genomes, how they are kept under tight control and can be unleashed thereby contributing to genome plasticity and environmental adaptation.
Max ERC Funding
1 490 876 €
Duration
Start date: 2010-10-01, End date: 2015-09-30
Project acronym MALARES
Project Genetics of Resistance to Malaria Parasites in the Mosquito Anopheles gambiae
Researcher (PI) Stephanie Blandin
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Anopheles gambiae mosquitoes are major vectors of Plasmodium falciparum, a protozoan parasite that causes the most severe form of human malaria in Africa. With an estimated 250 million infected people every year and another 3.3 billion at risk, malaria remains one of the biggest scourges of humanity. One of the promising approaches to fight malaria is the control of vector competence that determines the ability of a mosquito to transmit the disease. The fact that mosquito strains that are resistant to the parasites can be selected indicates that genetic factors in mosquitoes limit parasite development.
Here we propose to use laboratory infection models to decipher the complex genetic networks that sustain mosquito resistance to P. berghei and P. falciparum. In these models, genotype-to-genotype interactions and environmental variability are limited, two features that are essential to efficiently dissect the genetic control of a complex trait. The parallel identification of loci conferring resistance to P. berghei and to P. falciparum will be crucial to unravel the conserved and species-specific aspects of mosquito parasite interactions at the molecular level. We will further evaluate the contribution of the identified genes and networks to vector competence in natural mosquito populations. Because resistance naturally occurs in mosquito populations, this project has implications for the design of novel strategies and/or for the improvement of existing ones to reduce malaria transmission.
Summary
Anopheles gambiae mosquitoes are major vectors of Plasmodium falciparum, a protozoan parasite that causes the most severe form of human malaria in Africa. With an estimated 250 million infected people every year and another 3.3 billion at risk, malaria remains one of the biggest scourges of humanity. One of the promising approaches to fight malaria is the control of vector competence that determines the ability of a mosquito to transmit the disease. The fact that mosquito strains that are resistant to the parasites can be selected indicates that genetic factors in mosquitoes limit parasite development.
Here we propose to use laboratory infection models to decipher the complex genetic networks that sustain mosquito resistance to P. berghei and P. falciparum. In these models, genotype-to-genotype interactions and environmental variability are limited, two features that are essential to efficiently dissect the genetic control of a complex trait. The parallel identification of loci conferring resistance to P. berghei and to P. falciparum will be crucial to unravel the conserved and species-specific aspects of mosquito parasite interactions at the molecular level. We will further evaluate the contribution of the identified genes and networks to vector competence in natural mosquito populations. Because resistance naturally occurs in mosquito populations, this project has implications for the design of novel strategies and/or for the improvement of existing ones to reduce malaria transmission.
Max ERC Funding
1 489 600 €
Duration
Start date: 2011-06-01, End date: 2017-05-31
Project acronym MEIOSIGHT
Project MEIOtic inSIGHT: Deciphering the engine of heredity
Researcher (PI) Raphael Mercier
Host Institution (HI) INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Meiosis is an essential stage in the life cycle of sexually-reproducing organisms. Indeed, meiosis is the specialized cell division that reduces the number of chromosomes from two sets in the parent to one set in gametes, while fertilization restores the original chromosome number. Meiosis is also the stage of development when genetic recombination occurs, thus being the heart of Mendelian heredity. Increasing our knowledge on meiotic mechanisms, in addition to its intrinsic interest, may have also important implications for agriculture and medicine.
In the last decade Arabidopsis emerged as one of the prominent models in the field of meiosis. Indeed, the meiotic field benefits greatly from a multi-model approach with several kingdoms represented, highlighting both conserved mechanisms and variation around the theme. Arabidopsis did not emerge only as a representative of its phylum, but is also a very good model to study meiosis in general, notably because of the possibility of large scale genetic studies and the availability of large mutant collections and wide range of molecular and cytological tools. In this project we aim to use original approaches to decipher much further meiotic mechanisms, by isolating a large number of novel genes and characterizing their functions in an integrated manner. To identify new meiotic functions, we will use innovative genetic approaches. The first work package is based on a new suppressor screen strategy, taking advantage of a unique and favourable situation in Arabidopsis. The second is an unprecedented screen that exploits the fact that we can now synthesize haploids in a higher eukaryote. The third work package aims to fully exploit the available transcriptome data. In the fourth work package we will use these new genes to deeply decipher the meiotic mechanisms in an integrated manner.
Summary
Meiosis is an essential stage in the life cycle of sexually-reproducing organisms. Indeed, meiosis is the specialized cell division that reduces the number of chromosomes from two sets in the parent to one set in gametes, while fertilization restores the original chromosome number. Meiosis is also the stage of development when genetic recombination occurs, thus being the heart of Mendelian heredity. Increasing our knowledge on meiotic mechanisms, in addition to its intrinsic interest, may have also important implications for agriculture and medicine.
In the last decade Arabidopsis emerged as one of the prominent models in the field of meiosis. Indeed, the meiotic field benefits greatly from a multi-model approach with several kingdoms represented, highlighting both conserved mechanisms and variation around the theme. Arabidopsis did not emerge only as a representative of its phylum, but is also a very good model to study meiosis in general, notably because of the possibility of large scale genetic studies and the availability of large mutant collections and wide range of molecular and cytological tools. In this project we aim to use original approaches to decipher much further meiotic mechanisms, by isolating a large number of novel genes and characterizing their functions in an integrated manner. To identify new meiotic functions, we will use innovative genetic approaches. The first work package is based on a new suppressor screen strategy, taking advantage of a unique and favourable situation in Arabidopsis. The second is an unprecedented screen that exploits the fact that we can now synthesize haploids in a higher eukaryote. The third work package aims to fully exploit the available transcriptome data. In the fourth work package we will use these new genes to deeply decipher the meiotic mechanisms in an integrated manner.
Max ERC Funding
1 492 663 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym Micromecca
Project Molecular mechanisms underlying plant miRNA action
Researcher (PI) Anders Peter Brodersen
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary MicroRNAs (miRNAs) are 20-22 nt non-coding RNAs that regulate gene expression post transcriptionally via base pairing to complementary target mRNAs. They have fundamental importance for development and stress adaptation in plants and animals. Although a molecular frame work for miRNA biogenesis, degradation and action has been established, many aspects of this important gene regulatory pathway remain unknown. This project explores four main points. First, we propose to use genetic approaches to identify factors required for translational repression by miRNAs in plants. This mode of action was until recently thought to occur only exceptionally in plants. My post doctoral work showed that it occurs in many miRNA-target interactions. The mechanism remains unknown, however, leaving open a fertile area of investigation. Second, we wish to test specific hypotheses regarding the in vivo role of miRNA mediated endonucleolysis of mRNA targets. Long believed to serve exclusively as a degradation mechanism, we propose to test whether this process could have important functions in biogenesis of long non-coding RNA derived from mRNAs.
Third, my postdoctoral work has provided unique material to use molecular genetics to explore pathways responsible for miRNA degradation, an aspect of miRNA biology that only now is emerging as being of major importance. Finally, our unpublished results show that plant miRNAs and their associated effector protein Argonaute (AGO) are associated with membranes and that membrane association is crucial for function. This is in line with similar data recently obtained from different animal systems. We propose to use genetic, biochemical and cell biological approaches to clarify to which membrane compartment AGO and miRNAs are associated, how they are recruited to this compartment, and what the precise function of membrane association is.
These innovative approaches promise to give fundamental new insights into the inner workings of the pathway.
Summary
MicroRNAs (miRNAs) are 20-22 nt non-coding RNAs that regulate gene expression post transcriptionally via base pairing to complementary target mRNAs. They have fundamental importance for development and stress adaptation in plants and animals. Although a molecular frame work for miRNA biogenesis, degradation and action has been established, many aspects of this important gene regulatory pathway remain unknown. This project explores four main points. First, we propose to use genetic approaches to identify factors required for translational repression by miRNAs in plants. This mode of action was until recently thought to occur only exceptionally in plants. My post doctoral work showed that it occurs in many miRNA-target interactions. The mechanism remains unknown, however, leaving open a fertile area of investigation. Second, we wish to test specific hypotheses regarding the in vivo role of miRNA mediated endonucleolysis of mRNA targets. Long believed to serve exclusively as a degradation mechanism, we propose to test whether this process could have important functions in biogenesis of long non-coding RNA derived from mRNAs.
Third, my postdoctoral work has provided unique material to use molecular genetics to explore pathways responsible for miRNA degradation, an aspect of miRNA biology that only now is emerging as being of major importance. Finally, our unpublished results show that plant miRNAs and their associated effector protein Argonaute (AGO) are associated with membranes and that membrane association is crucial for function. This is in line with similar data recently obtained from different animal systems. We propose to use genetic, biochemical and cell biological approaches to clarify to which membrane compartment AGO and miRNAs are associated, how they are recruited to this compartment, and what the precise function of membrane association is.
These innovative approaches promise to give fundamental new insights into the inner workings of the pathway.
Max ERC Funding
1 459 011 €
Duration
Start date: 2012-01-01, End date: 2016-12-31
Project acronym REPODDID
Project Regulation of Polycomb Complex (PRC2) during development and in diseases
Researcher (PI) Raphaël, Florent Chaffrey Margueron
Host Institution (HI) INSTITUT CURIE
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Polycomb Group (PcG) proteins are pivotal for the specification and maintenance of cell identity by preventing inappropriate gene activation. They function mostly through the regulation of chromatin structure and, in particular, the post-translational modification of histones. Although the enzymatic activities of the main PcG complexes has been described, lots remain to be discovered in terms of how these chromatin modifying activities are regulated. Genome wide analysis uncovered genes that are targeted by PcG proteins in various model cell lines, however it still very unclear how PcG proteins are targeted to a specific set of genes depending on the cell type. Finally, PcG proteins are frequently fund deregulated in diseases among which cancer but whether the alteration of their expression is a causative event to pathologies requires further investigation.
This proposal is focused on the Polycomb Repressive Complex 2 (PRC2) whose function is pivotal to the polycomb machinery. In the first two aims of this proposal, we will investigate mechanistically how transcription factors, non-coding RNAs and chromatin structure might independently or in conjunction establish the conditions conducive to gene targeting by PRC2 and regulate its activity. In the third and fourth aims of this proposal, we will investigate what is the function of PRC2 during tumorigenesis and cell reprogramming and how its function is regulated during these processes.
Summary
Polycomb Group (PcG) proteins are pivotal for the specification and maintenance of cell identity by preventing inappropriate gene activation. They function mostly through the regulation of chromatin structure and, in particular, the post-translational modification of histones. Although the enzymatic activities of the main PcG complexes has been described, lots remain to be discovered in terms of how these chromatin modifying activities are regulated. Genome wide analysis uncovered genes that are targeted by PcG proteins in various model cell lines, however it still very unclear how PcG proteins are targeted to a specific set of genes depending on the cell type. Finally, PcG proteins are frequently fund deregulated in diseases among which cancer but whether the alteration of their expression is a causative event to pathologies requires further investigation.
This proposal is focused on the Polycomb Repressive Complex 2 (PRC2) whose function is pivotal to the polycomb machinery. In the first two aims of this proposal, we will investigate mechanistically how transcription factors, non-coding RNAs and chromatin structure might independently or in conjunction establish the conditions conducive to gene targeting by PRC2 and regulate its activity. In the third and fourth aims of this proposal, we will investigate what is the function of PRC2 during tumorigenesis and cell reprogramming and how its function is regulated during these processes.
Max ERC Funding
1 499 815 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym SIGHT
Project Systems Genetics of Heritable variaTions
Researcher (PI) Gael Yvert
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary The complexity by which genotypes modulate phenotypic variation has been a major obstacle in understanding the basis of inter-individual differences. In the particular case of disease susceptibility, enormous efforts have been conducted among large consortia of quantitative geneticists, and a recent wealth of results showed both victories and frustrations. Victories because many genetic factors could successfully be linked to diabetes, heart failure, cancer, infectivity, and many other common diseases. Frustrations as it is becoming more and more apparent that genetic dissections are far from completion, with many unsolved questions especially regarding gene x environment interactions and incomplete penetrance. In this context, I propose to revisit the molecular basis of phenotypic diversity by addressing fundamental questions in a simple and powerful model organism: the yeast S. cerevisiae.
Combining experimental biology and bioinformatics into a ‘systems’ approach, I propose 1) To reconsider our current view of genetic determinism. By examining the effect of genetic variation on single-cells, we will visualise how they shape probability laws underlying phenotypic outcomes. This will prepare us to the upcoming era of generalized single-cell analysis. 2) To investigate how chromatin epigenotypes affect phenotypic variations. We will characterize nucleosomal epi-polymorphisms and study their impact on transcriptional and phenotypic responses to environmental changes. This will establish whether and how individual epigenomes should be considered when planning trait dissections.
This ambitious project is grounded on solid preliminary results and can be achieved thanks to my dual expertise in numerical science and experimental genetics. The questions addressed are fundamental for our understanding of living systems and the innovative methodology will help us integrate upcoming technologies into the construction of personalized medicine.
Summary
The complexity by which genotypes modulate phenotypic variation has been a major obstacle in understanding the basis of inter-individual differences. In the particular case of disease susceptibility, enormous efforts have been conducted among large consortia of quantitative geneticists, and a recent wealth of results showed both victories and frustrations. Victories because many genetic factors could successfully be linked to diabetes, heart failure, cancer, infectivity, and many other common diseases. Frustrations as it is becoming more and more apparent that genetic dissections are far from completion, with many unsolved questions especially regarding gene x environment interactions and incomplete penetrance. In this context, I propose to revisit the molecular basis of phenotypic diversity by addressing fundamental questions in a simple and powerful model organism: the yeast S. cerevisiae.
Combining experimental biology and bioinformatics into a ‘systems’ approach, I propose 1) To reconsider our current view of genetic determinism. By examining the effect of genetic variation on single-cells, we will visualise how they shape probability laws underlying phenotypic outcomes. This will prepare us to the upcoming era of generalized single-cell analysis. 2) To investigate how chromatin epigenotypes affect phenotypic variations. We will characterize nucleosomal epi-polymorphisms and study their impact on transcriptional and phenotypic responses to environmental changes. This will establish whether and how individual epigenomes should be considered when planning trait dissections.
This ambitious project is grounded on solid preliminary results and can be achieved thanks to my dual expertise in numerical science and experimental genetics. The questions addressed are fundamental for our understanding of living systems and the innovative methodology will help us integrate upcoming technologies into the construction of personalized medicine.
Max ERC Funding
1 499 660 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym SMINSULATOR
Project Unveiling the Roles of Chromatin Insulators in Higher-order Chromatin Architecture and Transcription Regulation one molecule at a time
Researcher (PI) Marcelo Nollmann Martinez
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Eukaryotic chromosomes are condensed into several hierarchical levels of complexity: DNA is wrapped around core histones to form nucleosomes, nucleosomes form a higher-order structure called chromatin, and chromatin is subsequently organized by long-range contacts. The conformation of chromatin at these three levels greatly influences DNA transcription. One class of chromatin regulatory proteins called insulator factors set up boundaries between heterochromatin and euchromatin and generate long-range loops. In Drosophila, three types of insulators (Su(Hw), dCTCF and BEAF) have been shown to regulate transcription and organize chromatin at the higher level by the formation of long-range interactions that were proposed to be mediated by the coalescence of several insulator proteins into clusters (insulator bodies). Our research aims to unravel the mechanism by which insulator bodies dynamically regulate chromatin structure and transcription by using single-molecule biophysics and quantitative modeling. On one hand, we will apply novel super-resolution fluorescence microscopy methods to investigate the structure and assembly dynamics of insulator bodies in single cells throughout the cell cycle and the role of their regulatory partners. On the other hand, we will reconstitute the looping activity of insulators in vitro and apply single-molecule manipulation methods to gain detailed insights into the molecular mechanisms involved in defining and regulating chromatin organization by insulators. This project has the potential to impact our understanding of several fundamental cellular processes: transcription regulation, cell-cycle dynamics, higher-order chromatin organization, and cell differentiation. The methods developed here will be directly applicable to the investigation of other nuclear super-structures, such as transcription and replication factories and Polycomb bodies, and thus will impact other research areas, such as DNA replication, transcription and cell division.
Summary
Eukaryotic chromosomes are condensed into several hierarchical levels of complexity: DNA is wrapped around core histones to form nucleosomes, nucleosomes form a higher-order structure called chromatin, and chromatin is subsequently organized by long-range contacts. The conformation of chromatin at these three levels greatly influences DNA transcription. One class of chromatin regulatory proteins called insulator factors set up boundaries between heterochromatin and euchromatin and generate long-range loops. In Drosophila, three types of insulators (Su(Hw), dCTCF and BEAF) have been shown to regulate transcription and organize chromatin at the higher level by the formation of long-range interactions that were proposed to be mediated by the coalescence of several insulator proteins into clusters (insulator bodies). Our research aims to unravel the mechanism by which insulator bodies dynamically regulate chromatin structure and transcription by using single-molecule biophysics and quantitative modeling. On one hand, we will apply novel super-resolution fluorescence microscopy methods to investigate the structure and assembly dynamics of insulator bodies in single cells throughout the cell cycle and the role of their regulatory partners. On the other hand, we will reconstitute the looping activity of insulators in vitro and apply single-molecule manipulation methods to gain detailed insights into the molecular mechanisms involved in defining and regulating chromatin organization by insulators. This project has the potential to impact our understanding of several fundamental cellular processes: transcription regulation, cell-cycle dynamics, higher-order chromatin organization, and cell differentiation. The methods developed here will be directly applicable to the investigation of other nuclear super-structures, such as transcription and replication factories and Polycomb bodies, and thus will impact other research areas, such as DNA replication, transcription and cell division.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
