Project acronym CELLDOCTOR
Project Quantitative understanding of a living system and its engineering as a cellular organelle
Researcher (PI) Luis Serrano
Host Institution (HI) FUNDACIO CENTRE DE REGULACIO GENOMICA
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary The idea of harnessing living organisms for treating human diseases is not new but, so far, the majority of the living vectors used in human therapy are viruses which have the disadvantage of the limited number of genes and networks that can contain. Bacteria allow the cloning of complex networks and the possibility of making a large plethora of compounds, naturally or through careful redesign. One of the main limitations for the use of bacteria to treat human diseases is their complexity, the existence of a cell wall that difficult the communication with the target cells, the lack of control over its growth and the immune response that will elicit on its target. Ideally one would like to have a very small bacterium (of a mitochondria size), with no cell wall, which could be grown in Vitro, be genetically manipulated, for which we will have enough data to allow a complete understanding of its behaviour and which could live as a human cell parasite. Such a microorganism could in principle be used as a living vector in which genes of interests, or networks producing organic molecules of medical relevance, could be introduced under in Vitro conditions and then inoculated on extracted human cells or in the organism, and then become a new organelle in the host. Then, it could produce and secrete into the host proteins which will be needed to correct a genetic disease, or drugs needed by the patient. To do that, we need to understand in excruciating detail the Biology of the target bacterium and how to interface with the host cell cycle (Systems biology aspect). Then we need to have engineering tools (network design, protein design, simulations) to modify the target bacterium to behave like an organelle once inside the cell (Synthetic biology aspect). M.pneumoniae could be such a bacterium. It is one of the smallest free-living bacterium known (680 genes), has no cell wall, can be cultivated in Vitro, can be genetically manipulated and can enter inside human cells.
Summary
The idea of harnessing living organisms for treating human diseases is not new but, so far, the majority of the living vectors used in human therapy are viruses which have the disadvantage of the limited number of genes and networks that can contain. Bacteria allow the cloning of complex networks and the possibility of making a large plethora of compounds, naturally or through careful redesign. One of the main limitations for the use of bacteria to treat human diseases is their complexity, the existence of a cell wall that difficult the communication with the target cells, the lack of control over its growth and the immune response that will elicit on its target. Ideally one would like to have a very small bacterium (of a mitochondria size), with no cell wall, which could be grown in Vitro, be genetically manipulated, for which we will have enough data to allow a complete understanding of its behaviour and which could live as a human cell parasite. Such a microorganism could in principle be used as a living vector in which genes of interests, or networks producing organic molecules of medical relevance, could be introduced under in Vitro conditions and then inoculated on extracted human cells or in the organism, and then become a new organelle in the host. Then, it could produce and secrete into the host proteins which will be needed to correct a genetic disease, or drugs needed by the patient. To do that, we need to understand in excruciating detail the Biology of the target bacterium and how to interface with the host cell cycle (Systems biology aspect). Then we need to have engineering tools (network design, protein design, simulations) to modify the target bacterium to behave like an organelle once inside the cell (Synthetic biology aspect). M.pneumoniae could be such a bacterium. It is one of the smallest free-living bacterium known (680 genes), has no cell wall, can be cultivated in Vitro, can be genetically manipulated and can enter inside human cells.
Max ERC Funding
2 400 000 €
Duration
Start date: 2009-03-01, End date: 2015-02-28
Project acronym ENVGENE
Project Dissection of environmentally-mediated epigenetic silencing
Researcher (PI) Caroline Dean
Host Institution (HI) JOHN INNES CENTRE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary We intend to achieve a step change in our understanding of the mechanistic basis of epigenetic regulation. We will capitalize on a plant epigenetic silencing system, vernalization, which has many features that allow the complete dissection of different facets of epigenetic regulation. In addition, the silencing is quantitatively modulated by the environment enabling dissection of how external cues mediate epigenetic silencing. We will combine genetics, molecular biology and biochemical approaches with computational modelling to allow us to translate the extensive nuts and bolts information into an understanding of how the engine works. A particular strength of modelling will be its predictive nature and ability to distinguish between key components and those with subsidiary or redundant roles. The system we will use is vernalization, the cold-induced Polycomb-silencing of the target locus, FLC. We will dissect the many phases of vernalization: the triggering of FLC repression by prolonged cold; the nucleation and epigenetic stability of chromatin changes at FLC; and the spreading of the silencing yet spatial restriction to FLC. Our goal will be a full understanding of the complexity involved in the epigenetic silencing of this locus, described in a quantitative model that reveals how the silencing is induced by temperature and how individual components of the silencing network are integrated into a robust whole. This ambitious goal, which will uncover fundamental concepts important to gene regulation in many organisms, will be achieved through a tight integration of molecular analysis and computational modelling, enabling efficient cycling between experimentation, prediction and validation.
Summary
We intend to achieve a step change in our understanding of the mechanistic basis of epigenetic regulation. We will capitalize on a plant epigenetic silencing system, vernalization, which has many features that allow the complete dissection of different facets of epigenetic regulation. In addition, the silencing is quantitatively modulated by the environment enabling dissection of how external cues mediate epigenetic silencing. We will combine genetics, molecular biology and biochemical approaches with computational modelling to allow us to translate the extensive nuts and bolts information into an understanding of how the engine works. A particular strength of modelling will be its predictive nature and ability to distinguish between key components and those with subsidiary or redundant roles. The system we will use is vernalization, the cold-induced Polycomb-silencing of the target locus, FLC. We will dissect the many phases of vernalization: the triggering of FLC repression by prolonged cold; the nucleation and epigenetic stability of chromatin changes at FLC; and the spreading of the silencing yet spatial restriction to FLC. Our goal will be a full understanding of the complexity involved in the epigenetic silencing of this locus, described in a quantitative model that reveals how the silencing is induced by temperature and how individual components of the silencing network are integrated into a robust whole. This ambitious goal, which will uncover fundamental concepts important to gene regulation in many organisms, will be achieved through a tight integration of molecular analysis and computational modelling, enabling efficient cycling between experimentation, prediction and validation.
Max ERC Funding
2 450 000 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym FLYINGPOLYCOMB
Project Polycomb in development, genome regulation and cancer
Researcher (PI) Giacomo Cavalli
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Polycomb group (PcG) and trithorax group (trxG) genes were discovered in Drosophila melanogaster as repressors and activators of Hox genes, a set of transcription factors that specify the antero-posterior axis of the body plan. PcG and trxG proteins form multimeric complexes that are required to maintain their expression state after the initial transcriptional regulators disappear from the embryo. Subsequent work led to a better understanding of their mechanisms of action. Moreover, PcG and trxG genes have also been identified in vertebrates, where they regulate Hox genes, they are involved in cell proliferation, stem cell identity and cancer, genomic imprinting in plants and mammals and X inactivation. PcG and trxG components form multimeric complexes. Some trxG and PcG components possess methyltransferase activities directed toward specific lysines of histone H3, whereas other trxG and PcG proteins interpret these histone marks. Recent studies have described the genomewide distribution of PcG proteins and of their related histone modification in Drosophila and other species. However, the PcG recruitment code to their target chromatin is still not understood, and the mechanism of PcG-mediated gene silencing is unclear. The formation of subnuclear silencing compartments might contribute to the stable repression of transcription. Drosophila PcG proteins have a speckled nuclear distribution and the number of these so-called PcG bodies is progressively reduced during development. We showed that multiple PREs can associate in the nucleus to enhance the strength of PcG-mediated silencing. However, we do not know how frequent is this clustering process and how important it is functionally at a genomewide level. Our project will tackle these questions by using a combination of genetics, developmental biology, cell biology, genomics and bioinformatic approaches, with the aim to gain an integrated understanding of the role of Polycomb and trithorax in biology
Summary
Polycomb group (PcG) and trithorax group (trxG) genes were discovered in Drosophila melanogaster as repressors and activators of Hox genes, a set of transcription factors that specify the antero-posterior axis of the body plan. PcG and trxG proteins form multimeric complexes that are required to maintain their expression state after the initial transcriptional regulators disappear from the embryo. Subsequent work led to a better understanding of their mechanisms of action. Moreover, PcG and trxG genes have also been identified in vertebrates, where they regulate Hox genes, they are involved in cell proliferation, stem cell identity and cancer, genomic imprinting in plants and mammals and X inactivation. PcG and trxG components form multimeric complexes. Some trxG and PcG components possess methyltransferase activities directed toward specific lysines of histone H3, whereas other trxG and PcG proteins interpret these histone marks. Recent studies have described the genomewide distribution of PcG proteins and of their related histone modification in Drosophila and other species. However, the PcG recruitment code to their target chromatin is still not understood, and the mechanism of PcG-mediated gene silencing is unclear. The formation of subnuclear silencing compartments might contribute to the stable repression of transcription. Drosophila PcG proteins have a speckled nuclear distribution and the number of these so-called PcG bodies is progressively reduced during development. We showed that multiple PREs can associate in the nucleus to enhance the strength of PcG-mediated silencing. However, we do not know how frequent is this clustering process and how important it is functionally at a genomewide level. Our project will tackle these questions by using a combination of genetics, developmental biology, cell biology, genomics and bioinformatic approaches, with the aim to gain an integrated understanding of the role of Polycomb and trithorax in biology
Max ERC Funding
2 200 000 €
Duration
Start date: 2009-09-01, End date: 2015-08-31
Project acronym GROWTHCONTROL
Project Dissecting the transcriptional mechanisms controlling growth during normal development and cancer
Researcher (PI) Anssi Jussi Nikolai Taipale
Host Institution (HI) KAROLINSKA INSTITUTET
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary The main scientific questions addressed in this proposal relate to the understanding of molecular mechanisms of growth control and cancer through the combined use of high-throughput technologies and computational biology. We aim to create a systems-level understanding of the cell cycle, and its regulation by physiological growth factors and oncogenes through the use high-throughput biology to identify all or the majority of genes that are essential for cell cycle progression, and by combining this dataset with computationally predicted and experimentally validated target genes of growth factors and oncogenic pathways. In my opinion, such systems biology approach is critical for understanding of growth control, as organ-specific growth control has proven particularly refractory to genetic dissection. Much of what we know about physiological mechanisms controlling cellular growth in mammals has been revealed by human cancer genetics. These studies have revealed that a large number of genes can contribute to aberrant cell growth; there are more than 300 genes that have been linked to cancer, and mutations found in cancer are often cell type specific ( oncogene preference , i.e. PTCH mutations in medulloblastoma, APC in colon cancer, TMPRSS2-ERG in prostate cancer), suggesting that different pathways in different cell lineages are coupled to the cell cycle machinery. We have preliminary evidence that hedgehog (Hh) and Wnt signals are directly coupled to expression of N-myc and c-Myc genes, but only in tissues and cell-types that display a proliferative response to these factors. Both classical molecular and developmental biology as well as high throughput and systems biological methods will be used for dissection of the molecular mechanism of this selectivity. If successful, these experiments would establish a principle explaining why particular mutations are extremely common in some tumor types but not found at all in others.
Summary
The main scientific questions addressed in this proposal relate to the understanding of molecular mechanisms of growth control and cancer through the combined use of high-throughput technologies and computational biology. We aim to create a systems-level understanding of the cell cycle, and its regulation by physiological growth factors and oncogenes through the use high-throughput biology to identify all or the majority of genes that are essential for cell cycle progression, and by combining this dataset with computationally predicted and experimentally validated target genes of growth factors and oncogenic pathways. In my opinion, such systems biology approach is critical for understanding of growth control, as organ-specific growth control has proven particularly refractory to genetic dissection. Much of what we know about physiological mechanisms controlling cellular growth in mammals has been revealed by human cancer genetics. These studies have revealed that a large number of genes can contribute to aberrant cell growth; there are more than 300 genes that have been linked to cancer, and mutations found in cancer are often cell type specific ( oncogene preference , i.e. PTCH mutations in medulloblastoma, APC in colon cancer, TMPRSS2-ERG in prostate cancer), suggesting that different pathways in different cell lineages are coupled to the cell cycle machinery. We have preliminary evidence that hedgehog (Hh) and Wnt signals are directly coupled to expression of N-myc and c-Myc genes, but only in tissues and cell-types that display a proliferative response to these factors. Both classical molecular and developmental biology as well as high throughput and systems biological methods will be used for dissection of the molecular mechanism of this selectivity. If successful, these experiments would establish a principle explaining why particular mutations are extremely common in some tumor types but not found at all in others.
Max ERC Funding
2 200 000 €
Duration
Start date: 2009-03-01, End date: 2014-02-28
Project acronym PROTEOMICS V3.0
Project Proteomics v3.0: Development, Implementation and Dissemination of a Third Generation Proteomics Technology
Researcher (PI) Rudolf Aebersold
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Quantitative proteomics is a key technology for the life sciences in general and for systems biology in particular. So far, however, technical limitations have made it impossible to analyze the complete proteome of any species. It is the general goal of this proposal to develop, implement, apply and disseminate a new proteomic strategy that has the potential to generate quantitative proteomic datasets at an unprecedented depth, throughput, accuracy and robustness. Specifically, the new technology will identify and quantify every protein in a proteome. The title of the project Proteomics v3.0 was chosen to indicate the transformation of proteomics into its third phase, after 2D gel electrophoresis and LC-MS/MS based shotgun proteomics. Proteomics v3.0 is based on two sequential steps, emulating the strategy that has been immensely successful in the genomic sciences. In the first step the proteomic space is completely mapped out to generate a proteomic resource that is akin to the genomic sequence database. In the second step rapid and accurate assays will be developed to unambiguously identify and quantify any protein of the respective proteome in a multitude of samples. These assays will be made publicly accessible to support quantitative proteomic studies in the respective species. The strategy will first be implemented and tested in the yeast S. cerevisiae. In a later stage of the project it will be extended to the more complicated human proteome and include the development of assays that also probe the state of modification, splice forms and other types of protein variants generated by a specific open reading frame. Overall, the project will transform quantitative proteomics from a highly specialized technology practiced at a high level in a few laboratories worldwide into a commodity technology accessible, in principle to every group.
Summary
Quantitative proteomics is a key technology for the life sciences in general and for systems biology in particular. So far, however, technical limitations have made it impossible to analyze the complete proteome of any species. It is the general goal of this proposal to develop, implement, apply and disseminate a new proteomic strategy that has the potential to generate quantitative proteomic datasets at an unprecedented depth, throughput, accuracy and robustness. Specifically, the new technology will identify and quantify every protein in a proteome. The title of the project Proteomics v3.0 was chosen to indicate the transformation of proteomics into its third phase, after 2D gel electrophoresis and LC-MS/MS based shotgun proteomics. Proteomics v3.0 is based on two sequential steps, emulating the strategy that has been immensely successful in the genomic sciences. In the first step the proteomic space is completely mapped out to generate a proteomic resource that is akin to the genomic sequence database. In the second step rapid and accurate assays will be developed to unambiguously identify and quantify any protein of the respective proteome in a multitude of samples. These assays will be made publicly accessible to support quantitative proteomic studies in the respective species. The strategy will first be implemented and tested in the yeast S. cerevisiae. In a later stage of the project it will be extended to the more complicated human proteome and include the development of assays that also probe the state of modification, splice forms and other types of protein variants generated by a specific open reading frame. Overall, the project will transform quantitative proteomics from a highly specialized technology practiced at a high level in a few laboratories worldwide into a commodity technology accessible, in principle to every group.
Max ERC Funding
2 400 000 €
Duration
Start date: 2009-04-01, End date: 2014-03-31
Project acronym REGULATORYCIRCUITS
Project Novel Systematic Strategies for Elucidating Cellular Regulatory Circuits
Researcher (PI) Nir Friedman
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary The precise regulation of gene expression has been the subject of extensive scrutiny. Nonetheless, there is a big gap between genomic characterization of transcriptional responses and our predictions based on known molecular mechanisms and networks and of transcription regulation. In this proposal I argue for an approach to bridge this gap by using a novel experimental strategy that exploits the recent maturation of two technologies: the use of fluorescence reporter techniques to monitor promoter activity and high-throughput genetic manipulations for the construction of combinatorial genetic perturbations. By combining these, we will screen for genes that modulate the transcriptional response of target promoters, use genetic interactions between them to better resolve their functional dependencies, and build detailed quantitative models of transcriptional processes. We will use the budding yeast model organism, which allows for efficient manipulations, to dissect two transcriptional responses that are prototypical of many regulatory networks in living cells: [1] The early response to osmotic stress, which is mediated by at least two signaling pathways and multiple transcription factors, and [2] the central carbon metabolism response to shifts in carbon source, which involves multiple sensing and signaling pathways to maintain homeostasis. Our approach will elucidate mechanisms that are opaque to classical screens and facilitate building detailed predictive models of these responses. These results will lead to understanding of general principles that govern transcriptional networks. This is the first approach to comprehensively characterize the molecular mechanisms that modulate a transcriptional response, and arrange them in a coherent network. It will open many questions for detailed biochemical investigations, as well as set the stage to extend these ideas to use more detailed phenotypic assays and in more complex organisms.
Summary
The precise regulation of gene expression has been the subject of extensive scrutiny. Nonetheless, there is a big gap between genomic characterization of transcriptional responses and our predictions based on known molecular mechanisms and networks and of transcription regulation. In this proposal I argue for an approach to bridge this gap by using a novel experimental strategy that exploits the recent maturation of two technologies: the use of fluorescence reporter techniques to monitor promoter activity and high-throughput genetic manipulations for the construction of combinatorial genetic perturbations. By combining these, we will screen for genes that modulate the transcriptional response of target promoters, use genetic interactions between them to better resolve their functional dependencies, and build detailed quantitative models of transcriptional processes. We will use the budding yeast model organism, which allows for efficient manipulations, to dissect two transcriptional responses that are prototypical of many regulatory networks in living cells: [1] The early response to osmotic stress, which is mediated by at least two signaling pathways and multiple transcription factors, and [2] the central carbon metabolism response to shifts in carbon source, which involves multiple sensing and signaling pathways to maintain homeostasis. Our approach will elucidate mechanisms that are opaque to classical screens and facilitate building detailed predictive models of these responses. These results will lead to understanding of general principles that govern transcriptional networks. This is the first approach to comprehensively characterize the molecular mechanisms that modulate a transcriptional response, and arrange them in a coherent network. It will open many questions for detailed biochemical investigations, as well as set the stage to extend these ideas to use more detailed phenotypic assays and in more complex organisms.
Max ERC Funding
2 199 899 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym REVOLUTION
Project RNA silencing in regulation and evolution
Researcher (PI) David Baulcombe
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Small RNA is a specificity determinant of silencing mechanisms that can target RNA through base pairing to affect RNA stability and translation. This targeting process, directly or indirectly, can also target DNA and chromatin to introduce epigenetic modifications. In plants there are many hundreds of thousands - of different small silencing RNAs (sRNAs) produced from many thousands of loci. These sRNAs have enormous potential to influence genetic and epigenetic regulation because, from analysis of transgenes, it is clear that RNA silencing can have diverse effects. There can be RNA-mediated signalling between cells and complex interaction networks of RNA molecules with positive feedback and amplification loops. In addition there can be epigenetic effects that, once induced, can persist between generations. In REVOLUTION the aim is to find out which of the endogenous sRNAs have the various RNA silencing properties revealed by transgenes. The aim is then to integrate these findings into a systems level understanding of regulation and evolution in Arabidopsis. The role of these sRNA systems will be investigated in plants subjected to hormone and stress treatments. We shall also investigate the role of these sRNAs in natural variation between genotypes of plant and their effect in hybrids between these plants. In the final stages of the work it is intended to explore the various effects of endogenous sRNAs in plants other than Arabidopsis including tomato. This work will provide a new level of understanding of the mechanisms affecting gene expression in plants. This fundamental new understanding will affect crop science through conventional breeding and genetic engineering. In addition because RNA silencing takes place in animals including vertebrates there will be relevance of this work beyond plants.
Summary
Small RNA is a specificity determinant of silencing mechanisms that can target RNA through base pairing to affect RNA stability and translation. This targeting process, directly or indirectly, can also target DNA and chromatin to introduce epigenetic modifications. In plants there are many hundreds of thousands - of different small silencing RNAs (sRNAs) produced from many thousands of loci. These sRNAs have enormous potential to influence genetic and epigenetic regulation because, from analysis of transgenes, it is clear that RNA silencing can have diverse effects. There can be RNA-mediated signalling between cells and complex interaction networks of RNA molecules with positive feedback and amplification loops. In addition there can be epigenetic effects that, once induced, can persist between generations. In REVOLUTION the aim is to find out which of the endogenous sRNAs have the various RNA silencing properties revealed by transgenes. The aim is then to integrate these findings into a systems level understanding of regulation and evolution in Arabidopsis. The role of these sRNA systems will be investigated in plants subjected to hormone and stress treatments. We shall also investigate the role of these sRNAs in natural variation between genotypes of plant and their effect in hybrids between these plants. In the final stages of the work it is intended to explore the various effects of endogenous sRNAs in plants other than Arabidopsis including tomato. This work will provide a new level of understanding of the mechanisms affecting gene expression in plants. This fundamental new understanding will affect crop science through conventional breeding and genetic engineering. In addition because RNA silencing takes place in animals including vertebrates there will be relevance of this work beyond plants.
Max ERC Funding
2 298 433 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym RIBOGENES
Project The role of noncoding RNA in sense and antisense or orientation in epigenetic control of rRNA genes
Researcher (PI) Ingrid Grummt
Host Institution (HI) DEUTSCHES KREBSFORSCHUNGSZENTRUM HEIDELBERG
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Non-coding RNAs (ncRNAs) play a significant role in the control of gene expression and epigenetic regulation. It seems that ncRNAs might be numerous and highly adapted in roles that require specific nucleic acid recognition without complex catalysis, such as in guiding RNA modifications or in directing post-transcriptional regulation of gene expression and chromatin structure. Our previous work has revealed that NoRC, a chromatin remodeling complex that triggers heterochromatin formation and transcriptional silencing of a fraction of rRNA genes, is associated with 100-250 nt RNAs that originate from the intergenic spacer (IGS) separating rDNA repeats. Furthermore, a fraction of rDNA is transcribed in antisense orientation. Both IGS RNA and antisense transcripts display a growth- and tissue-specific expression pattern. The goal of this project is to decipher the role of NoRC-associated RNA in alterations of chromatin structure and epigenetic control of rDNA. Our research will focus on the synthesis, regulation, and processing of intergenic and antisense transcripts in response to cell growth and differentiation as well as on the role of NoRC-associated RNA in epigenetic regulation of rRNA genes. The following points will be addressed: (1) Deciphering the mechanism underlying RNA-directed establishment of specific epigenetic marks and formation of silent chromatin domains, (2) Functional analysis of posttranscriptional modifications that regulate RNA binding and NoRC activity, (3) Identification of non-ribosomal target genes of NoRC, and (4) Elucidation of the link between transcriptional activity and active demethylation of the rDNA promoter. Given the fact that basic regulatory principles are conserved throughout evolution, this work will have a great impact on our understanding of RNA-directed silencing mechanisms and will reveal how epigenetic defects cause human diseases.
Summary
Non-coding RNAs (ncRNAs) play a significant role in the control of gene expression and epigenetic regulation. It seems that ncRNAs might be numerous and highly adapted in roles that require specific nucleic acid recognition without complex catalysis, such as in guiding RNA modifications or in directing post-transcriptional regulation of gene expression and chromatin structure. Our previous work has revealed that NoRC, a chromatin remodeling complex that triggers heterochromatin formation and transcriptional silencing of a fraction of rRNA genes, is associated with 100-250 nt RNAs that originate from the intergenic spacer (IGS) separating rDNA repeats. Furthermore, a fraction of rDNA is transcribed in antisense orientation. Both IGS RNA and antisense transcripts display a growth- and tissue-specific expression pattern. The goal of this project is to decipher the role of NoRC-associated RNA in alterations of chromatin structure and epigenetic control of rDNA. Our research will focus on the synthesis, regulation, and processing of intergenic and antisense transcripts in response to cell growth and differentiation as well as on the role of NoRC-associated RNA in epigenetic regulation of rRNA genes. The following points will be addressed: (1) Deciphering the mechanism underlying RNA-directed establishment of specific epigenetic marks and formation of silent chromatin domains, (2) Functional analysis of posttranscriptional modifications that regulate RNA binding and NoRC activity, (3) Identification of non-ribosomal target genes of NoRC, and (4) Elucidation of the link between transcriptional activity and active demethylation of the rDNA promoter. Given the fact that basic regulatory principles are conserved throughout evolution, this work will have a great impact on our understanding of RNA-directed silencing mechanisms and will reveal how epigenetic defects cause human diseases.
Max ERC Funding
831 756 €
Duration
Start date: 2009-03-01, End date: 2014-02-28
Project acronym SCG
Project Systematic Chemical Genetic Interrogation of Biological Networks
Researcher (PI) Michael David Tyers
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Recent genome-scale studies have revealed the massive redundancies and functional interconnectivities encoded by the genome. For example, the budding yeast Saccharomyces cerevisiae is predicted to harbor 200,000 synthetic lethal interactions. This genetic density has profound implications for both understanding the architecture of living systems and drug discovery. In particular, the dense connections of biological networks mandate a multi-node strategy to selectively manipulate any given biological response, whether it be to probe system level properties or for therapeutic intervention in human disease. By analogy to Ehrlich s magic bullet concept, we term this approach the magic shotgun . We propose to systematically identify chemical-genetic interactions that selectively disrupt any specific mutant genotype and chemical-chemical interactions that selectively kill pathogenic species. Our five main objectives are: (i) construct a comprehensive Chemical Genetic Matrix (CGM) of small molecule-gene interactions in order to predict chemical synergies and manipulate network function in a species-specific manner; (ii) elaborate the CGM with a set of ~5,000 yeast bioactive molecules derived from high throughput/high content screens; (iii) identify small molecule combinations that modulate stem cell and cancer cell renewal and differentiation; (iv) define compound mechanisms of action by functional genomics; (v) integrate chemical-genetic, genetic and protein interaction datasets to predict gene function, small molecule targets and network properties. This research will cross-connect genetic pathways through chemical space, identify species-specific combinations of agents as therapeutic leads and provide a repository of small molecule probes for cell biological and systems-level analysis. The principles developed through the course of this work will raise our understanding of biological networks and help establish a new approach to drug discovery.
Summary
Recent genome-scale studies have revealed the massive redundancies and functional interconnectivities encoded by the genome. For example, the budding yeast Saccharomyces cerevisiae is predicted to harbor 200,000 synthetic lethal interactions. This genetic density has profound implications for both understanding the architecture of living systems and drug discovery. In particular, the dense connections of biological networks mandate a multi-node strategy to selectively manipulate any given biological response, whether it be to probe system level properties or for therapeutic intervention in human disease. By analogy to Ehrlich s magic bullet concept, we term this approach the magic shotgun . We propose to systematically identify chemical-genetic interactions that selectively disrupt any specific mutant genotype and chemical-chemical interactions that selectively kill pathogenic species. Our five main objectives are: (i) construct a comprehensive Chemical Genetic Matrix (CGM) of small molecule-gene interactions in order to predict chemical synergies and manipulate network function in a species-specific manner; (ii) elaborate the CGM with a set of ~5,000 yeast bioactive molecules derived from high throughput/high content screens; (iii) identify small molecule combinations that modulate stem cell and cancer cell renewal and differentiation; (iv) define compound mechanisms of action by functional genomics; (v) integrate chemical-genetic, genetic and protein interaction datasets to predict gene function, small molecule targets and network properties. This research will cross-connect genetic pathways through chemical space, identify species-specific combinations of agents as therapeutic leads and provide a repository of small molecule probes for cell biological and systems-level analysis. The principles developed through the course of this work will raise our understanding of biological networks and help establish a new approach to drug discovery.
Max ERC Funding
2 400 000 €
Duration
Start date: 2009-08-01, End date: 2014-07-31
Project acronym SYSTEM_US
Project Systems Biology of Human Metabolism
Researcher (PI) Bernhard Örn Palsson
Host Institution (HI) HASKOLI ISLANDS
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Whole-genome sequences and their annotation have enabled the reconstruction of genome-scale metabolic networks. Such network reconstructions form the foundation for systems analysis of metabolic functions in health and disease. Over the past ten years, a series of genome-scale reconstructions have been built for microorganisms. They have been demonstrated to be useful for developing a deeper understanding of physiological processes, drive discovery through computer generated hypothesis relating to missing parts of a network, to interpret the consequences of gene knock outs, and for metabolic engineering and bioprocess purposes. With build-35 of the human genome sequence it has proved to be possible to initiate the build of a similar genome-scale reconstruction of metabolism in man. Thus an era of systems biology analysis of human metabolic functions has just been opened, in an analogous fashion as happened for microorganisms about 10 years ago. This proposal describes a program that will lead this new era. Our three overall objectives are: 1) to continue to build the metabolic reconstruction in an iterative fashion as has been done for microorganisms in the past, 2) to deploy existing computer algorithms to systematically fill in gaps in our knowledge base about human metabolism, and 3) to use the reconstruction high-throughput data analysis and to begin the effort of drug screening and discovery for metabolic interventions. The PI has been active in this field for over 25 years, and, in fact, has been a leader in developing reconstruction technology, the computer methods that are used to characterize them, and bring them to practical uses. He has been particularly active in training young scientist in this field and been involved in translational research and company startups.
Summary
Whole-genome sequences and their annotation have enabled the reconstruction of genome-scale metabolic networks. Such network reconstructions form the foundation for systems analysis of metabolic functions in health and disease. Over the past ten years, a series of genome-scale reconstructions have been built for microorganisms. They have been demonstrated to be useful for developing a deeper understanding of physiological processes, drive discovery through computer generated hypothesis relating to missing parts of a network, to interpret the consequences of gene knock outs, and for metabolic engineering and bioprocess purposes. With build-35 of the human genome sequence it has proved to be possible to initiate the build of a similar genome-scale reconstruction of metabolism in man. Thus an era of systems biology analysis of human metabolic functions has just been opened, in an analogous fashion as happened for microorganisms about 10 years ago. This proposal describes a program that will lead this new era. Our three overall objectives are: 1) to continue to build the metabolic reconstruction in an iterative fashion as has been done for microorganisms in the past, 2) to deploy existing computer algorithms to systematically fill in gaps in our knowledge base about human metabolism, and 3) to use the reconstruction high-throughput data analysis and to begin the effort of drug screening and discovery for metabolic interventions. The PI has been active in this field for over 25 years, and, in fact, has been a leader in developing reconstruction technology, the computer methods that are used to characterize them, and bring them to practical uses. He has been particularly active in training young scientist in this field and been involved in translational research and company startups.
Max ERC Funding
2 399 634 €
Duration
Start date: 2009-03-01, End date: 2014-08-31
