Project acronym CLEAR
Project Modulating cellular clearance to cure human disease
Researcher (PI) Andrea Ballabio
Host Institution (HI) FONDAZIONE TELETHON
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary Cellular clearance is a fundamental process required by all cells in all species. Important physiological processes, such as aging, and pathological mechanisms, such as neurodegeneration, are strictly dependent on cellular clearance. In eukaryotes, most of the cellular clearing processes occur in a specialized organelle, the lysosome. This project is based on a recent discovery, made in our laboratory, of a gene network, which we have named CLEAR, that controls lysosomal biogenesis and function and regulates cellular clearance. The specific goals of the project are: 1) the comprehensive characterization of the mechanisms underlying the CLEAR network, 2) the thorough understanding of CLEAR physiological function at the cellular and organism levels, 3) the development of strategies and tools to modulate cellular clearance, and 4) the implementation of proof-of-principle therapeutic studies based on the activation of the CLEAR network in murine models of human lysosomal storage disorders and of neurodegenerative diseases, such as Alzheimers s and Huntington s diseases. A combination of genomics, bioinformatics, systems biology, chemical genomics, cell biology, and mouse genetics approaches will be used to achieve these goals. Our goal is to develop tools to modulate cellular clearance and to use such tools to develop therapies to cure human disease. The potential medical relevance of this project is very high, particularly in the field of neurodegenerative disease. Therapies that prevent, ameliorate or delay neurodegeneration in these diseases would have a huge impact on human health.
Summary
Cellular clearance is a fundamental process required by all cells in all species. Important physiological processes, such as aging, and pathological mechanisms, such as neurodegeneration, are strictly dependent on cellular clearance. In eukaryotes, most of the cellular clearing processes occur in a specialized organelle, the lysosome. This project is based on a recent discovery, made in our laboratory, of a gene network, which we have named CLEAR, that controls lysosomal biogenesis and function and regulates cellular clearance. The specific goals of the project are: 1) the comprehensive characterization of the mechanisms underlying the CLEAR network, 2) the thorough understanding of CLEAR physiological function at the cellular and organism levels, 3) the development of strategies and tools to modulate cellular clearance, and 4) the implementation of proof-of-principle therapeutic studies based on the activation of the CLEAR network in murine models of human lysosomal storage disorders and of neurodegenerative diseases, such as Alzheimers s and Huntington s diseases. A combination of genomics, bioinformatics, systems biology, chemical genomics, cell biology, and mouse genetics approaches will be used to achieve these goals. Our goal is to develop tools to modulate cellular clearance and to use such tools to develop therapies to cure human disease. The potential medical relevance of this project is very high, particularly in the field of neurodegenerative disease. Therapies that prevent, ameliorate or delay neurodegeneration in these diseases would have a huge impact on human health.
Max ERC Funding
2 100 000 €
Duration
Start date: 2010-03-01, End date: 2015-02-28
Project acronym DARCGENS
Project Derived and Ancestral RNAs: Comparative Genomics and Evolution of ncRNAs
Researcher (PI) Christopher Paul Ponting
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary Much light has been shed on the number, mechanisms and functions of protein-coding genes in the human genome. In comparison, we know almost nothing about the origins and mechanisms of the functional dark matter , including sequence that is transcribed outside of protein-coding gene loci. This interdisciplinary proposal will capitalize on new theoretical and experimental opportunities to establish the extent by which long non-coding RNAs contribute to mammalian and fruit fly biology. Since 2001, the Ponting group has pioneered the comparative analysis of protein-coding genes across the amniotes and Drosophilids within many international genome sequencing consortia. This Advanced Grant will break new ground by applying these approaches to long intergenic non-coding RNA (lincRNA) genes from mammals to birds and to flies. The Grant will allow Ponting to free himself of the constraints normally associated with in silico analyses by analysing lincRNAs in vitro and in vivo. The integration of computational and experimental approaches for lincRNAs from across the metazoan tree provides a powerful new toolkit for elucidating the origins and biological roles of these enigmatic molecules. Catalogues of lincRNA loci will be built for human, mouse, fruit fly, zebrafinch, chicken and Aplysia by exploiting data from next-generation sequencing technologies. This will immediately provide a new perspective on how these loci arise, evolve and function, including whether their orthologues are apparent across diverse species. Using new evidence that lincRNA loci act in cis with neighbouring protein-coding loci, we will determine lincRNA mechanisms and will establish the consequences of lincRNA knock-down, knock-out and over-expression in mouse, chick and fruitfly.
Summary
Much light has been shed on the number, mechanisms and functions of protein-coding genes in the human genome. In comparison, we know almost nothing about the origins and mechanisms of the functional dark matter , including sequence that is transcribed outside of protein-coding gene loci. This interdisciplinary proposal will capitalize on new theoretical and experimental opportunities to establish the extent by which long non-coding RNAs contribute to mammalian and fruit fly biology. Since 2001, the Ponting group has pioneered the comparative analysis of protein-coding genes across the amniotes and Drosophilids within many international genome sequencing consortia. This Advanced Grant will break new ground by applying these approaches to long intergenic non-coding RNA (lincRNA) genes from mammals to birds and to flies. The Grant will allow Ponting to free himself of the constraints normally associated with in silico analyses by analysing lincRNAs in vitro and in vivo. The integration of computational and experimental approaches for lincRNAs from across the metazoan tree provides a powerful new toolkit for elucidating the origins and biological roles of these enigmatic molecules. Catalogues of lincRNA loci will be built for human, mouse, fruit fly, zebrafinch, chicken and Aplysia by exploiting data from next-generation sequencing technologies. This will immediately provide a new perspective on how these loci arise, evolve and function, including whether their orthologues are apparent across diverse species. Using new evidence that lincRNA loci act in cis with neighbouring protein-coding loci, we will determine lincRNA mechanisms and will establish the consequences of lincRNA knock-down, knock-out and over-expression in mouse, chick and fruitfly.
Max ERC Funding
2 400 000 €
Duration
Start date: 2010-05-01, End date: 2015-04-30
Project acronym DECODE
Project Decoding the complexity of quantitative natural variation in Arabidopsis thaliana
Researcher (PI) Olivier Loudet
Host Institution (HI) INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT
Call Details Starting Grant (StG), LS2, ERC-2009-StG
Summary Following a long history of quantitative genetics in crop plants, it now becomes feasible to use naturally-occuring variation contained in Arabidopsis thaliana accessions (lines isolated from natural populations) as the source of quantitative genomics approaches, designed to map QTLs and resolve them at the gene level. Apart from being able to exploit in multiple genetic backgrounds allelic variation that cannot be easily generated by conventional mutagenesis, the (relatively few) success of the QTL studies has often been because of the use of quantitative phenotyping, as opposed to the qualitative gauges used in typical mutant screens. Among the various genetic mechanisms responsible for natural variation that have just started to be revealed, cis-acting regulation is potentially of large impact, despite remaining more difficult to recognize and confirm. The objective of this project is to apply genome-wide quantitative molecular genetics to both, a very integrative and classical quantitative trait (growth in interaction with the environment) and a molecular trait a priori more directly linked to the source of variation (gene expression under cis-regulation). We propose to use a combination of our unique high-troughput phenotyping robot, fine-mapping, complementation approaches and association genetics to pinpoint a significant number of QTLs and eQTLs to the gene level and identify causative polymorphisms and the molecular variation controlling natural diversity. Working at an unprecedented scale should finally allow to resolve enough quantitative loci and pay a significant contribution to drawing a general picture as to how and where in the pathways adaptation is shaping natural variation and improve our understanding of the transcriptional cis-regulatory code.
Summary
Following a long history of quantitative genetics in crop plants, it now becomes feasible to use naturally-occuring variation contained in Arabidopsis thaliana accessions (lines isolated from natural populations) as the source of quantitative genomics approaches, designed to map QTLs and resolve them at the gene level. Apart from being able to exploit in multiple genetic backgrounds allelic variation that cannot be easily generated by conventional mutagenesis, the (relatively few) success of the QTL studies has often been because of the use of quantitative phenotyping, as opposed to the qualitative gauges used in typical mutant screens. Among the various genetic mechanisms responsible for natural variation that have just started to be revealed, cis-acting regulation is potentially of large impact, despite remaining more difficult to recognize and confirm. The objective of this project is to apply genome-wide quantitative molecular genetics to both, a very integrative and classical quantitative trait (growth in interaction with the environment) and a molecular trait a priori more directly linked to the source of variation (gene expression under cis-regulation). We propose to use a combination of our unique high-troughput phenotyping robot, fine-mapping, complementation approaches and association genetics to pinpoint a significant number of QTLs and eQTLs to the gene level and identify causative polymorphisms and the molecular variation controlling natural diversity. Working at an unprecedented scale should finally allow to resolve enough quantitative loci and pay a significant contribution to drawing a general picture as to how and where in the pathways adaptation is shaping natural variation and improve our understanding of the transcriptional cis-regulatory code.
Max ERC Funding
1 742 113 €
Duration
Start date: 2010-02-01, End date: 2016-01-31
Project acronym DEPICT
Project Design principles and controllability of protein circuits
Researcher (PI) Uri Alon
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary Cells use circuits of interacting proteins to respond to their environment. In the past decades, molecular biology has provided detailed knowledge on the proteins in these circuits and their interactions. To fully understand circuit function requires, in addition to molecular knowledge, new concepts that explain how multiple components work together to perform systems level functions. Our lab has been a leader in defining such concepts, based on combined experimental and theoretical study of well characterized circuits in bacteria and human cells. In this proposal we aim to find novel principles on how circuits resist fluctuations and errors, and how they can be controlled by drugs: (1) Why do key regulatory systems use bifunctional enzymes that catalyze antagonistic reactions (e.g. both kinase and phosphatase)? We will test the role of bifunctional enzymes in making circuits robust to variations in protein levels. (2) Why are some genes regulated by a repressor and others by an activator? We will test this in the context of reduction of errors in transcription control. (3) Are there principles that describe how drugs combine to affect protein dynamics in human cells? We will use a novel dynamic proteomics approach developed in our lab to explore how protein dynamics can be controlled by drug combinations. This research will define principles that unite our understanding of seemingly distinct biological systems, and explain their particular design in terms of systems-level functions. This understanding will help form the basis for a future medicine that rationally controls the state of the cell based on a detailed blueprint of their circuit design, and quantitative principles for the effects of drugs on this circuitry.
Summary
Cells use circuits of interacting proteins to respond to their environment. In the past decades, molecular biology has provided detailed knowledge on the proteins in these circuits and their interactions. To fully understand circuit function requires, in addition to molecular knowledge, new concepts that explain how multiple components work together to perform systems level functions. Our lab has been a leader in defining such concepts, based on combined experimental and theoretical study of well characterized circuits in bacteria and human cells. In this proposal we aim to find novel principles on how circuits resist fluctuations and errors, and how they can be controlled by drugs: (1) Why do key regulatory systems use bifunctional enzymes that catalyze antagonistic reactions (e.g. both kinase and phosphatase)? We will test the role of bifunctional enzymes in making circuits robust to variations in protein levels. (2) Why are some genes regulated by a repressor and others by an activator? We will test this in the context of reduction of errors in transcription control. (3) Are there principles that describe how drugs combine to affect protein dynamics in human cells? We will use a novel dynamic proteomics approach developed in our lab to explore how protein dynamics can be controlled by drug combinations. This research will define principles that unite our understanding of seemingly distinct biological systems, and explain their particular design in terms of systems-level functions. This understanding will help form the basis for a future medicine that rationally controls the state of the cell based on a detailed blueprint of their circuit design, and quantitative principles for the effects of drugs on this circuitry.
Max ERC Funding
2 261 440 €
Duration
Start date: 2010-03-01, End date: 2015-02-28
Project acronym EPIGENETIX
Project Epigenetic regulation and monoallelic gene expression: the X-inactivation paradigm and beyond
Researcher (PI) Edith Heard
Host Institution (HI) INSTITUT CURIE
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary X-chromosome inactivation (XCI) represents a classic example of epigenetics in mammals. In this process, one of the two X chromosomes in females is converted from an active into a clonally heritable, inactive, state during early embryonic development, to ensure dosage compensation between the sexes. This process is also remarkable in that an entire chromosome is silenced while its homologue, present in the same nucleus, remains active. Thus, in addition to being an epigenetics paradigm, XCI also represents a powerful model for monoallelic gene expression and could provide important insights into the mechanisms underlying other examples of random, monoallelic regulation. The key locus underlying the initiation of XCI is the X-inactivation centre (Xic). The Xic ensures the induction and monoallelic expression of a non-coding RNA (Xist) that is responsible for triggering chromosomal silencing in cis during development. We would like to understand the mechanisms underlying the Xic's functions and define whether other, Xic-like loci exist in the genome. Once XCI is established, the inactive state is initially reversible but becomes progressively locked in as development proceeds due to numerous epigenetic marks such as DNA methylation and histone modifications, as well as nuclear compartmentalization and asynchronous replication. In the proposed program, we will exploit our expertise in XCI to develop new lines of research and use novel technologies to investigate monoallelic gene expression, nuclear organization and epigenetics during development. Our main objectives are (1) to understand how monoallelic expression states are established and maintained during early development and (2) to assess how chromosome dynamics and nuclear architecture can impact on these states.
Summary
X-chromosome inactivation (XCI) represents a classic example of epigenetics in mammals. In this process, one of the two X chromosomes in females is converted from an active into a clonally heritable, inactive, state during early embryonic development, to ensure dosage compensation between the sexes. This process is also remarkable in that an entire chromosome is silenced while its homologue, present in the same nucleus, remains active. Thus, in addition to being an epigenetics paradigm, XCI also represents a powerful model for monoallelic gene expression and could provide important insights into the mechanisms underlying other examples of random, monoallelic regulation. The key locus underlying the initiation of XCI is the X-inactivation centre (Xic). The Xic ensures the induction and monoallelic expression of a non-coding RNA (Xist) that is responsible for triggering chromosomal silencing in cis during development. We would like to understand the mechanisms underlying the Xic's functions and define whether other, Xic-like loci exist in the genome. Once XCI is established, the inactive state is initially reversible but becomes progressively locked in as development proceeds due to numerous epigenetic marks such as DNA methylation and histone modifications, as well as nuclear compartmentalization and asynchronous replication. In the proposed program, we will exploit our expertise in XCI to develop new lines of research and use novel technologies to investigate monoallelic gene expression, nuclear organization and epigenetics during development. Our main objectives are (1) to understand how monoallelic expression states are established and maintained during early development and (2) to assess how chromosome dynamics and nuclear architecture can impact on these states.
Max ERC Funding
2 860 000 €
Duration
Start date: 2010-05-01, End date: 2015-10-31
Project acronym EPINCRNA
Project Epigenetic and genome stability: non coding RNA-mediated chromatin modifications in S. cerevisiae
Researcher (PI) Antonin Morillon
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS2, ERC-2009-StG
Summary Our project is to understand the role of non coding (nc)RNA in the regulation of epigenetic landscape and gene expression. RNA interference pathway is absent in the budding yeast but recent works from our laboratory showed the existence of an original ncRNA-dependent pathway that controls gene expression in S. cerevisiae. We characterized a cryptic unstable ncRNA mediating the transcriptional silencing of the transposon Ty1 through histone methylation. Furthermore, unpublished data suggest the existence of subtelomeric ncRNAs that might control telomere metabolism and promoter-associated ncRNAs that mediate repressive epigenetic marks. We propose that a class of unstable ncRNA mediates genome expression and fluidity through histone modifications. Following 2 directions, our aim is to systematically identify these ncRNAs (A) and further characterize their regulatory mechanisms (B). (A) First, we aim to identify the regulatory ncRNAs by performing genome-wide approaches in strains accumulating these regulatory ncRNAs. We envisage developing protocols to analyze the cryptic transcriptome using deep sequencing technologies. (B) Second, we will further characterize the previously identified regulatory ncRNAs controlling repetitive regions (Ty1 transposon and telomeric repeats) but also gene expression. Through a range of experimental procedures from living cell biology (Fluorescence Immuno Hybridization), biochemical approaches (RNA-TRAP) and genetic, we will determine the dynamics of the regulatory ncRNA within the cell, the associated proteins that regulate their activities and the chromatin defects resulting from their expression. Our aim is to extensively describe the RNAi-like regulation in S. cerevisiae, that we anticipate to be broadly conserved in other eukaryotes.
Summary
Our project is to understand the role of non coding (nc)RNA in the regulation of epigenetic landscape and gene expression. RNA interference pathway is absent in the budding yeast but recent works from our laboratory showed the existence of an original ncRNA-dependent pathway that controls gene expression in S. cerevisiae. We characterized a cryptic unstable ncRNA mediating the transcriptional silencing of the transposon Ty1 through histone methylation. Furthermore, unpublished data suggest the existence of subtelomeric ncRNAs that might control telomere metabolism and promoter-associated ncRNAs that mediate repressive epigenetic marks. We propose that a class of unstable ncRNA mediates genome expression and fluidity through histone modifications. Following 2 directions, our aim is to systematically identify these ncRNAs (A) and further characterize their regulatory mechanisms (B). (A) First, we aim to identify the regulatory ncRNAs by performing genome-wide approaches in strains accumulating these regulatory ncRNAs. We envisage developing protocols to analyze the cryptic transcriptome using deep sequencing technologies. (B) Second, we will further characterize the previously identified regulatory ncRNAs controlling repetitive regions (Ty1 transposon and telomeric repeats) but also gene expression. Through a range of experimental procedures from living cell biology (Fluorescence Immuno Hybridization), biochemical approaches (RNA-TRAP) and genetic, we will determine the dynamics of the regulatory ncRNA within the cell, the associated proteins that regulate their activities and the chromatin defects resulting from their expression. Our aim is to extensively describe the RNAi-like regulation in S. cerevisiae, that we anticipate to be broadly conserved in other eukaryotes.
Max ERC Funding
1 735 524 €
Duration
Start date: 2009-12-01, End date: 2014-11-30
Project acronym FUNCTIONAL GENOMICS
Project DISSECTING GENETIC DEPENDENCIES IN CANCER
Researcher (PI) René Bernards
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary While significant progress has been made in the diagnosis and treatment of cancer, several major issues remain unresolved. First, only a minority of patients respond to most forms of (chemo)therapy. It is generally believed that this poor responsiveness to drugs has its origin, at least in part, in the molecular heterogeneity of cancer. This heterogeneity requires the use of biomarkers to stratify patients having seemingly similar tumors according to their likely responses to specific cancer therapies. To identify such biomarkers, we will use large-scale genetic screens to identify genes that are causally involved in controlling responses to cancer drugs. Such genes are likely biomarkers of drug responsiveness in the clinic. Availability of such drug response biomarkers will facilitate a more personalized therapy choice for each individual patient. A second major deficit in effective cancer therapy is the lack of sufficient highly selective drug targets. The large-scale cancer genome re-sequencing efforts already indicate that there is a paucity of druggable genes that are consistently mutated in cancer and the same holds true for genes that are consistently over-expressed in cancer. Hence, there is an urgent need for innovative drug targets that have a similar cancer-selectivity as the genes that are specifically mutated or over-expressed in cancer. In this project, we will use large-scale loss of function genetic screens, exploiting the concept of synthetic lethality , to identify genes whose inactivation is selectively toxic to cells having a defined cancer-specific genetic alteration. Drugs against these targets will be highly cancer-selective, as their activity hinges on the presence of a specific genetic defect, which is only present in the cancer cell.
Summary
While significant progress has been made in the diagnosis and treatment of cancer, several major issues remain unresolved. First, only a minority of patients respond to most forms of (chemo)therapy. It is generally believed that this poor responsiveness to drugs has its origin, at least in part, in the molecular heterogeneity of cancer. This heterogeneity requires the use of biomarkers to stratify patients having seemingly similar tumors according to their likely responses to specific cancer therapies. To identify such biomarkers, we will use large-scale genetic screens to identify genes that are causally involved in controlling responses to cancer drugs. Such genes are likely biomarkers of drug responsiveness in the clinic. Availability of such drug response biomarkers will facilitate a more personalized therapy choice for each individual patient. A second major deficit in effective cancer therapy is the lack of sufficient highly selective drug targets. The large-scale cancer genome re-sequencing efforts already indicate that there is a paucity of druggable genes that are consistently mutated in cancer and the same holds true for genes that are consistently over-expressed in cancer. Hence, there is an urgent need for innovative drug targets that have a similar cancer-selectivity as the genes that are specifically mutated or over-expressed in cancer. In this project, we will use large-scale loss of function genetic screens, exploiting the concept of synthetic lethality , to identify genes whose inactivation is selectively toxic to cells having a defined cancer-specific genetic alteration. Drugs against these targets will be highly cancer-selective, as their activity hinges on the presence of a specific genetic defect, which is only present in the cancer cell.
Max ERC Funding
2 176 000 €
Duration
Start date: 2010-06-01, End date: 2015-05-31
Project acronym FUNCTIONALEDGE
Project Determining the roles of the nuclear periphery in mammalian genome function
Researcher (PI) Wendy Bickmore
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary DNA sequence and epigenetic chromatin maps are important in understanding how genomes are regulated. However, these maps are linear and do not account for the three-dimensional context within which the genome functions in the cell. The spatial organisation of the genome in the nucleus is not random and is conserved in evolution, implying that it is under functional selection. This proposal aims to determine the functional significance of positioning specific genome regions at the edge of the nucleus in mammalian cells. The nuclear periphery has conventionally been considered as a zone of inactive chromatin and transcriptional repression. Several regulatory gene loci move away from the nuclear periphery as they are activated during differentiation. Novel approaches, developed by ourselves and others, that allow genomic regions to be relocated from the centre of the nucleus to the periphery, have directly shown that proximity to the nuclear edge can down-regulate human gene expression. We propose to dissect the pathways that mediate this spatially-defined transcriptional regulation, to determine what features make certain genes susceptible to it, to establish the functional consequences of preventing gene repositioning during differentiation, and to examine defects of the periphery found in premature ageing. A neglected hypothesis is that positioning of inactive chromatin against the nuclear periphery is a mechanism to minimize DNA damage on sequences in the nuclear centre. We will determine whether mutation rate is altered when loci are repositioned towards the nuclear periphery. By experimentally remodelling the spatial organisation of the genome, this proposal goes beyond the current descriptive phase of 3D nuclear organisation, into an understanding of its functional consequences on multiple aspects of genome function. It will also aid in understanding human diseases characterised by alterations of the nuclear periphery.
Summary
DNA sequence and epigenetic chromatin maps are important in understanding how genomes are regulated. However, these maps are linear and do not account for the three-dimensional context within which the genome functions in the cell. The spatial organisation of the genome in the nucleus is not random and is conserved in evolution, implying that it is under functional selection. This proposal aims to determine the functional significance of positioning specific genome regions at the edge of the nucleus in mammalian cells. The nuclear periphery has conventionally been considered as a zone of inactive chromatin and transcriptional repression. Several regulatory gene loci move away from the nuclear periphery as they are activated during differentiation. Novel approaches, developed by ourselves and others, that allow genomic regions to be relocated from the centre of the nucleus to the periphery, have directly shown that proximity to the nuclear edge can down-regulate human gene expression. We propose to dissect the pathways that mediate this spatially-defined transcriptional regulation, to determine what features make certain genes susceptible to it, to establish the functional consequences of preventing gene repositioning during differentiation, and to examine defects of the periphery found in premature ageing. A neglected hypothesis is that positioning of inactive chromatin against the nuclear periphery is a mechanism to minimize DNA damage on sequences in the nuclear centre. We will determine whether mutation rate is altered when loci are repositioned towards the nuclear periphery. By experimentally remodelling the spatial organisation of the genome, this proposal goes beyond the current descriptive phase of 3D nuclear organisation, into an understanding of its functional consequences on multiple aspects of genome function. It will also aid in understanding human diseases characterised by alterations of the nuclear periphery.
Max ERC Funding
1 701 090 €
Duration
Start date: 2010-03-01, End date: 2016-02-29
Project acronym HUCNC
Project Conserved Non-Coding Sequences; function, variability and phenotypic consequences
Researcher (PI) Stylianos Antonarakis
Host Institution (HI) UNIVERSITE DE GENEVE
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary Comparative genomics revealed that ~5% of the human genome is conserved among mammals. This fraction is likely functional, and could harbor pathogenic mutations. We have shown (Nature 2002, Science 2003) that more than half of the constrained fraction of the genome consists of Conserved Non-Coding sequences (CNCs). Model organisms provided evidence for enhancer activity for a fraction of CNCs; in addition another fraction is part of large non-coding RNAs (lincRNA). However, the function of the majority of CNCs is unknown. Importantly, a few pathogenic mutations in CNCs have been associated with genetic disorders. We propose to i) perform functional analysis of CNCs, and ii) identify the spectrum of pathogenic CNC mutations in recognizable human phenotypes. The aims are: 1. Functional genomic connectivity of CNCs 1a. Use 4C in CNCs in various cell types and determine their physical genomic interactions. 1b. Perform targeted disruption of CNCs in cells and assess the functional outcomes. 2. Pathogenic variation of CNCs 2a. Assess the common variation in CNCs: i) common deletion/insertions in 350 samples by aCGH of all human CNCs; ii) common SNP/small indels using DNA selection and High Throughput Sequencing (HTS) of CNCs in 100 samples. 2b. Identify likely pathogenic mutations in developmental syndromes. Search for i) large deletions and duplications of CNCs using aCGH in 1500 samples with malformation syndromes, 1000 from spontaneous abortions, and 500 with X-linked mental retardation; and ii) point mutations in these samples by targeted HTS. The distinction between pathogenic and non-pathogenic variants is difficult, and we propose approaches to meet the challenge. 3. Genetic control (cis and trans eQTLs) of expression variation of CNC lincRNAs, using 200 samples.
Summary
Comparative genomics revealed that ~5% of the human genome is conserved among mammals. This fraction is likely functional, and could harbor pathogenic mutations. We have shown (Nature 2002, Science 2003) that more than half of the constrained fraction of the genome consists of Conserved Non-Coding sequences (CNCs). Model organisms provided evidence for enhancer activity for a fraction of CNCs; in addition another fraction is part of large non-coding RNAs (lincRNA). However, the function of the majority of CNCs is unknown. Importantly, a few pathogenic mutations in CNCs have been associated with genetic disorders. We propose to i) perform functional analysis of CNCs, and ii) identify the spectrum of pathogenic CNC mutations in recognizable human phenotypes. The aims are: 1. Functional genomic connectivity of CNCs 1a. Use 4C in CNCs in various cell types and determine their physical genomic interactions. 1b. Perform targeted disruption of CNCs in cells and assess the functional outcomes. 2. Pathogenic variation of CNCs 2a. Assess the common variation in CNCs: i) common deletion/insertions in 350 samples by aCGH of all human CNCs; ii) common SNP/small indels using DNA selection and High Throughput Sequencing (HTS) of CNCs in 100 samples. 2b. Identify likely pathogenic mutations in developmental syndromes. Search for i) large deletions and duplications of CNCs using aCGH in 1500 samples with malformation syndromes, 1000 from spontaneous abortions, and 500 with X-linked mental retardation; and ii) point mutations in these samples by targeted HTS. The distinction between pathogenic and non-pathogenic variants is difficult, and we propose approaches to meet the challenge. 3. Genetic control (cis and trans eQTLs) of expression variation of CNC lincRNAs, using 200 samples.
Max ERC Funding
2 353 920 €
Duration
Start date: 2010-07-01, End date: 2015-06-30
Project acronym I-FIVE
Project Interferon-focused Innate Immunity Interactome and Inhibitome
Researcher (PI) Giulio Gino Maria Superti Furga
Host Institution (HI) CEMM - FORSCHUNGSZENTRUM FUER MOLEKULARE MEDIZIN GMBH
Call Details Advanced Grant (AdG), LS2, ERC-2009-AdG
Summary After a decade of development in model organisms and later in mammalian cells, mass spectrometry-based functional proteomics approaches have come of age and are ready to enable a systematic study of the innate immune system. We propose to cross the large-scale proteomics and innate immunity disciplines to obtain a functionally annotated map of the molecular machinery involved in viral recognition and leading to the hallmark interferon response, through a three-pronged approach: 1. Map the interactome of innate immunity proteins in macrophages to establish the network of components leading to interferon production; 2. Chart the interactions of molecular patterns, mostly nucleic acids, to identify the receptors and sensors at the non-self/self interface; 3. Study viral pathogenicity factors as molecular jammers of the anti-viral response and elucidate their mode of action to uncover critical nodes (inhibitome). Datasets are integrated and released at regular intervals with embargoed windows allowing a network of collaborators/own laboratory to do in-depth validation. New components at data intersections will be tested through loss-of-function experiments and standardized read-outs for the interferon pathway as well as genetic association with autoimmune diseases. Because of its unbiased/large scope and its cross-validating approaches, wherein the newly mapped circuitry is modeled, challenged by inducers and perturbed by viral agents, i-FIVE has the potential to promote a systems-level understanding of the interferon branch of molecular innate immunity. This insight may in turn create medical opportunities for the treatment of autoimmune disorders, septic shoc, arthritis as well as in boosting anti-viral responses.
Summary
After a decade of development in model organisms and later in mammalian cells, mass spectrometry-based functional proteomics approaches have come of age and are ready to enable a systematic study of the innate immune system. We propose to cross the large-scale proteomics and innate immunity disciplines to obtain a functionally annotated map of the molecular machinery involved in viral recognition and leading to the hallmark interferon response, through a three-pronged approach: 1. Map the interactome of innate immunity proteins in macrophages to establish the network of components leading to interferon production; 2. Chart the interactions of molecular patterns, mostly nucleic acids, to identify the receptors and sensors at the non-self/self interface; 3. Study viral pathogenicity factors as molecular jammers of the anti-viral response and elucidate their mode of action to uncover critical nodes (inhibitome). Datasets are integrated and released at regular intervals with embargoed windows allowing a network of collaborators/own laboratory to do in-depth validation. New components at data intersections will be tested through loss-of-function experiments and standardized read-outs for the interferon pathway as well as genetic association with autoimmune diseases. Because of its unbiased/large scope and its cross-validating approaches, wherein the newly mapped circuitry is modeled, challenged by inducers and perturbed by viral agents, i-FIVE has the potential to promote a systems-level understanding of the interferon branch of molecular innate immunity. This insight may in turn create medical opportunities for the treatment of autoimmune disorders, septic shoc, arthritis as well as in boosting anti-viral responses.
Max ERC Funding
1 974 022 €
Duration
Start date: 2010-04-01, End date: 2015-03-31
