Project acronym 2-HIT
Project Genetic interaction networks: From C. elegans to human disease
Researcher (PI) Ben Lehner
Host Institution (HI) FUNDACIO CENTRE DE REGULACIO GENOMICA
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Most hereditary diseases in humans are genetically complex, resulting from combinations of mutations in multiple genes. However synthetic interactions between genes are very difficult to identify in population studies because of a lack of statistical power and we fundamentally do not understand how mutations interact to produce phenotypes. C. elegans is a unique animal in which genetic interactions can be rapidly identified in vivo using RNA interference, and we recently used this system to construct the first genetic interaction network for any animal, focused on signal transduction genes. The first objective of this proposal is to extend this work and map a comprehensive genetic interaction network for this model metazoan. This project will provide the first insights into the global properties of animal genetic interaction networks, and a comprehensive view of the functional relationships between genes in an animal. The second objective of the proposal is to use C. elegans to develop and validate experimentally integrated gene networks that connect genes to phenotypes and predict genetic interactions on a genome-wide scale. The methods that we develop and validate in C. elegans will then be applied to predict phenotypes and interactions for human genes. The final objective is to dissect the molecular mechanisms underlying genetic interactions, and to understand how these interactions evolve. The combined aim of these three objectives is to generate a framework for understanding and predicting how mutations interact to produce phenotypes, including in human disease.
Summary
Most hereditary diseases in humans are genetically complex, resulting from combinations of mutations in multiple genes. However synthetic interactions between genes are very difficult to identify in population studies because of a lack of statistical power and we fundamentally do not understand how mutations interact to produce phenotypes. C. elegans is a unique animal in which genetic interactions can be rapidly identified in vivo using RNA interference, and we recently used this system to construct the first genetic interaction network for any animal, focused on signal transduction genes. The first objective of this proposal is to extend this work and map a comprehensive genetic interaction network for this model metazoan. This project will provide the first insights into the global properties of animal genetic interaction networks, and a comprehensive view of the functional relationships between genes in an animal. The second objective of the proposal is to use C. elegans to develop and validate experimentally integrated gene networks that connect genes to phenotypes and predict genetic interactions on a genome-wide scale. The methods that we develop and validate in C. elegans will then be applied to predict phenotypes and interactions for human genes. The final objective is to dissect the molecular mechanisms underlying genetic interactions, and to understand how these interactions evolve. The combined aim of these three objectives is to generate a framework for understanding and predicting how mutations interact to produce phenotypes, including in human disease.
Max ERC Funding
1 100 000 €
Duration
Start date: 2008-09-01, End date: 2014-04-30
Project acronym 4C
Project 4C technology: uncovering the multi-dimensional structure of the genome
Researcher (PI) Wouter Leonard De Laat
Host Institution (HI) KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary The architecture of DNA in the cell nucleus is an emerging epigenetic key contributor to genome function. We recently developed 4C technology, a high-throughput technique that combines state-of-the-art 3C technology with tailored micro-arrays to uniquely allow for an unbiased genome-wide search for DNA loci that interact in the nuclear space. Based on 4C technology, we were the first to provide a comprehensive overview of long-range DNA contacts of selected loci. The data showed that active and inactive chromatin domains contact many distinct regions within and between chromosomes and genes switch long-range DNA contacts in relation to their expression status. 4C technology not only allows investigating the three-dimensional structure of DNA in the nucleus, it also accurately reconstructs at least 10 megabases of the one-dimensional chromosome sequence map around the target sequence. Changes in this physical map as a result of genomic rearrangements are therefore identified by 4C technology. We recently demonstrated that 4C detects deletions, balanced inversions and translocations in patient samples at a resolution (~7kb) that allowed immediate sequencing of the breakpoints. Excitingly, 4C technology therefore offers the first high-resolution genomic approach that can identify both balanced and unbalanced genomic rearrangements. 4C is expected to become an important tool in clinical diagnosis and prognosis. Key objectives of this proposal are: 1. Explore the functional significance of DNA folding in the nucleus by systematically applying 4C technology to differentially expressed gene loci. 2. Adapt 4C technology such that it allows for massive parallel analysis of DNA interactions between regulatory elements and gene promoters. This method would greatly facilitate the identification of functionally relevant DNA elements in the genome. 3. Develop 4C technology into a clinical diagnostic tool for the accurate detection of balanced and unbalanced rearrangements.
Summary
The architecture of DNA in the cell nucleus is an emerging epigenetic key contributor to genome function. We recently developed 4C technology, a high-throughput technique that combines state-of-the-art 3C technology with tailored micro-arrays to uniquely allow for an unbiased genome-wide search for DNA loci that interact in the nuclear space. Based on 4C technology, we were the first to provide a comprehensive overview of long-range DNA contacts of selected loci. The data showed that active and inactive chromatin domains contact many distinct regions within and between chromosomes and genes switch long-range DNA contacts in relation to their expression status. 4C technology not only allows investigating the three-dimensional structure of DNA in the nucleus, it also accurately reconstructs at least 10 megabases of the one-dimensional chromosome sequence map around the target sequence. Changes in this physical map as a result of genomic rearrangements are therefore identified by 4C technology. We recently demonstrated that 4C detects deletions, balanced inversions and translocations in patient samples at a resolution (~7kb) that allowed immediate sequencing of the breakpoints. Excitingly, 4C technology therefore offers the first high-resolution genomic approach that can identify both balanced and unbalanced genomic rearrangements. 4C is expected to become an important tool in clinical diagnosis and prognosis. Key objectives of this proposal are: 1. Explore the functional significance of DNA folding in the nucleus by systematically applying 4C technology to differentially expressed gene loci. 2. Adapt 4C technology such that it allows for massive parallel analysis of DNA interactions between regulatory elements and gene promoters. This method would greatly facilitate the identification of functionally relevant DNA elements in the genome. 3. Develop 4C technology into a clinical diagnostic tool for the accurate detection of balanced and unbalanced rearrangements.
Max ERC Funding
1 225 000 €
Duration
Start date: 2008-09-01, End date: 2013-08-31
Project acronym CDNF
Project Compartmentalization and dynamics of Nuclear functions
Researcher (PI) Angela Taddei
Host Institution (HI) INSTITUT CURIE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary The eukaryotic genome is packaged into large-scale chromatin structures that occupy distinct domains in the nucleus and this organization is now seen as a key contributor to genome functions. Two key functions of the genome can take advantage of nuclear organization: regulated gene expression and the propagation of a stable genome. To understand these fundamental processes, we have chosen to use yeast as a model system that allows genetics, molecular biology and advanced live microscopy approaches to be combined. Budding yeast have been very powerful to demonstrate that gene position can play an active role in regulating gene expression. Distinct subcompartments dedicated to either gene silencing or activation of specific genes are positioned at the nuclear periphery. To gain insight into the mechanisms underlying this sub-compartmentalization, we will address three complementary issues: - What are the mechanisms involved in the establishment and maintenance of silent nuclear compartments? - How and why are some activated genes recruited to the nuclear periphery? - What are the relationships between repressive and activating nuclear compartments? Concerning the maintenance of genome integrity, recent advances in yeast highlight the importance of nuclear architecture. However, how nuclear organization influences the formation and processing of DNA lesions remain poorly understood. We will focus on two main questions: - How and where in the nucleus are double strand breaks recognized, processed, and repaired? - Where do breaks or gaps resulting from replicative stress at 'fragile sites' arise in the nucleus and how does nuclear organization influence their stability? We hope to gain a better understanding of the mechanisms presiding nuclear organization and its importance for genome functions. These mechanisms are likely to be conserved and will be subsequently tested in higher eukaryotic cells.
Summary
The eukaryotic genome is packaged into large-scale chromatin structures that occupy distinct domains in the nucleus and this organization is now seen as a key contributor to genome functions. Two key functions of the genome can take advantage of nuclear organization: regulated gene expression and the propagation of a stable genome. To understand these fundamental processes, we have chosen to use yeast as a model system that allows genetics, molecular biology and advanced live microscopy approaches to be combined. Budding yeast have been very powerful to demonstrate that gene position can play an active role in regulating gene expression. Distinct subcompartments dedicated to either gene silencing or activation of specific genes are positioned at the nuclear periphery. To gain insight into the mechanisms underlying this sub-compartmentalization, we will address three complementary issues: - What are the mechanisms involved in the establishment and maintenance of silent nuclear compartments? - How and why are some activated genes recruited to the nuclear periphery? - What are the relationships between repressive and activating nuclear compartments? Concerning the maintenance of genome integrity, recent advances in yeast highlight the importance of nuclear architecture. However, how nuclear organization influences the formation and processing of DNA lesions remain poorly understood. We will focus on two main questions: - How and where in the nucleus are double strand breaks recognized, processed, and repaired? - Where do breaks or gaps resulting from replicative stress at 'fragile sites' arise in the nucleus and how does nuclear organization influence their stability? We hope to gain a better understanding of the mechanisms presiding nuclear organization and its importance for genome functions. These mechanisms are likely to be conserved and will be subsequently tested in higher eukaryotic cells.
Max ERC Funding
1 000 000 €
Duration
Start date: 2008-09-01, End date: 2014-05-31
Project acronym CONSERVREGCIRCUITRY
Project Conservation and Divergence of Tissue-Specific Transcriptional Regulation
Researcher (PI) Duncan Odom
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Vertebrates contain hundreds of different cell types which maintain phenotypic identity by a combination of epigenetic programming and genomic regulation. Systems biology approaches are now used in a number of laboratories to determine how transcription factors and chromatin marks pattern the human genome. Despite high conservation of the cellular and molecular function of many mammalian transcription factors, our recent experiments in matched mouse and human tissues indicates that most transcription factor binding events to DNA are very poorly conserved. A hypothesis that could account for this apparent divergence is that the larger regional pattern of transcription factor binding may be conserved. To test this, (1) we are characterizing the global transcriptional profile, chromatin state, and complete genomic occupancy of a set of tissue-specific transcription factors in hepatocytes of strategically chosen mammals; (2) to further identify the precise mechanistic contribution of cis and trans effects, we are comparing transcription factor binding at homologous regions of human and mouse DNA in a mouse line that carries human chromosome 21. Together, these projects will provide insight into the general principles of how transcriptional networks are evolutionarily conserved to regulate cell fate specification and function using a clinically important cell type as a model.
Summary
Vertebrates contain hundreds of different cell types which maintain phenotypic identity by a combination of epigenetic programming and genomic regulation. Systems biology approaches are now used in a number of laboratories to determine how transcription factors and chromatin marks pattern the human genome. Despite high conservation of the cellular and molecular function of many mammalian transcription factors, our recent experiments in matched mouse and human tissues indicates that most transcription factor binding events to DNA are very poorly conserved. A hypothesis that could account for this apparent divergence is that the larger regional pattern of transcription factor binding may be conserved. To test this, (1) we are characterizing the global transcriptional profile, chromatin state, and complete genomic occupancy of a set of tissue-specific transcription factors in hepatocytes of strategically chosen mammals; (2) to further identify the precise mechanistic contribution of cis and trans effects, we are comparing transcription factor binding at homologous regions of human and mouse DNA in a mouse line that carries human chromosome 21. Together, these projects will provide insight into the general principles of how transcriptional networks are evolutionarily conserved to regulate cell fate specification and function using a clinically important cell type as a model.
Max ERC Funding
960 000 €
Duration
Start date: 2008-10-01, End date: 2013-09-30
Project acronym DSBREPAIR
Project Developmental and Genetic Analysis of DNA Double-Strand Break Repair
Researcher (PI) Marcel Tijsterman
Host Institution (HI) ACADEMISCH ZIEKENHUIS LEIDEN
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary The DNA within our cells is constantly being damaged by both environmental and endogenous agents; of the many forms of DNA damage, the DNA double-strand break (DSB) is considered to be most dangerous. Correct processing of DSBs is not only essential for maintaining genomic integrity but is also required in specific biological processes, such as meiotic recombination and V(D)J recombination, in which DNA breaks are deliberately generated. In animals, defects in the proper response to DSBs can thus have different outcomes: cancer predisposition, embryonic lethality, or compromised immunity. Many genes that play a role in the processing of DSBs have been identified over the past decades, mainly by cloning genes that are responsible for specific human genomic instability or immune deficiency syndromes, and by genetic approaches using unicellular eukaryotes and rodent cell lines. It is, however, evident that many components required in higher eukaryotes are not yet known and the identification of those will be a major challenge for future research. Here, we will for the first time systematically test all genes encoded by an animals genome directly for their involvement in the cellular response to DSB in both somatic and germline tissues: we will use our recently developed transgenic animal models (C. elegans) that visualizes repair of a single localized genomic DNA break in genome wide RNAi screenings to identify (and then characterize) the complement of genes that are required to keep our genome stable, and when mutated can predispose humans to cancer. In parallel, we will study the cellular response to single DNA breaks that are artificially generated during different stages of gametogenesis, as well as address the developmental consequences of DSB induction during the earliest stages of embryonic development – an almost completely unexplored area in the field of genome instability and DNA damage responses.
Summary
The DNA within our cells is constantly being damaged by both environmental and endogenous agents; of the many forms of DNA damage, the DNA double-strand break (DSB) is considered to be most dangerous. Correct processing of DSBs is not only essential for maintaining genomic integrity but is also required in specific biological processes, such as meiotic recombination and V(D)J recombination, in which DNA breaks are deliberately generated. In animals, defects in the proper response to DSBs can thus have different outcomes: cancer predisposition, embryonic lethality, or compromised immunity. Many genes that play a role in the processing of DSBs have been identified over the past decades, mainly by cloning genes that are responsible for specific human genomic instability or immune deficiency syndromes, and by genetic approaches using unicellular eukaryotes and rodent cell lines. It is, however, evident that many components required in higher eukaryotes are not yet known and the identification of those will be a major challenge for future research. Here, we will for the first time systematically test all genes encoded by an animals genome directly for their involvement in the cellular response to DSB in both somatic and germline tissues: we will use our recently developed transgenic animal models (C. elegans) that visualizes repair of a single localized genomic DNA break in genome wide RNAi screenings to identify (and then characterize) the complement of genes that are required to keep our genome stable, and when mutated can predispose humans to cancer. In parallel, we will study the cellular response to single DNA breaks that are artificially generated during different stages of gametogenesis, as well as address the developmental consequences of DSB induction during the earliest stages of embryonic development – an almost completely unexplored area in the field of genome instability and DNA damage responses.
Max ERC Funding
1 060 000 €
Duration
Start date: 2008-05-01, End date: 2014-04-30
Project acronym DTSSCP
Project Determinants of mammalian transcription start site selection and core promoter usage
Researcher (PI) Albin Sandelin
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Understanding the mechanisms underlying the initiation and regulation of transcription remains one of the most fundamental questions in biology. Much of what we know about the transcription process was inferred from experiments on a handful of genes. As these experiments are not realistically scalable, corresponding computational methods building on these findings have emerged; however, these are not accurate enough for annotation of genomes. The limitations reflect that we have no accurate universal model describing transcription initiation; to a large extent, our understanding is based on case stories. Recently, high-throughput methods have been developed to chart the TSS landscape with nucleotide resolution. Using these data, I have dissected promoters at nucleotide level and found patterns that explain the transcription initiation rate for individual nucleotides. The objective for this work is to extend this to the first universal model for how cells select core promoters and associated TSSs. This will have two counterparts: i)prediction of TSSs from DNA sequence given a region of accessible DNA, and ii)prediction of DNA accessibility based on DNA sequences and dynamic epigenetic factors. Such a model will be a corner stone of future experimental and computational transcriptome and gene regulation studies.
Summary
Understanding the mechanisms underlying the initiation and regulation of transcription remains one of the most fundamental questions in biology. Much of what we know about the transcription process was inferred from experiments on a handful of genes. As these experiments are not realistically scalable, corresponding computational methods building on these findings have emerged; however, these are not accurate enough for annotation of genomes. The limitations reflect that we have no accurate universal model describing transcription initiation; to a large extent, our understanding is based on case stories. Recently, high-throughput methods have been developed to chart the TSS landscape with nucleotide resolution. Using these data, I have dissected promoters at nucleotide level and found patterns that explain the transcription initiation rate for individual nucleotides. The objective for this work is to extend this to the first universal model for how cells select core promoters and associated TSSs. This will have two counterparts: i)prediction of TSSs from DNA sequence given a region of accessible DNA, and ii)prediction of DNA accessibility based on DNA sequences and dynamic epigenetic factors. Such a model will be a corner stone of future experimental and computational transcriptome and gene regulation studies.
Max ERC Funding
812 399 €
Duration
Start date: 2008-09-01, End date: 2013-08-31
Project acronym EPIGEPLAS
Project Epigenetic determinants of the genome that govern cellular plasticity
Researcher (PI) Dirk Schübeler
Host Institution (HI) FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH FONDATION
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Differentiation events in mammalian development involve stable resetting of transcriptional programs, which entails changes in the epigenetic state of target sequences defined by modifications of DNA and bound nucleosomes. These recently identified epigenetic layers modulate DNA accessibility in a positive and negative manner and thus could make genetic readouts context-dependent and dynamic. The proposed project aims to quantify the epigenetic contribution to cellular differentiation as a key event in development. By applying parallel genomic approaches we will comprehensively define the epigenome and its plasticity during cellular commitment of pluripotent murine stem cells into defined terminally differentiated cells. We will focus on DNA methylation and its interplay with several histone modifications as a way to achieve stable gene silencing. The resulting global profiles will gain insights into targeting principles and generate statistical, predictive models of regulation. From these mechanistic models will be derived and tested by genetically interfering with genetic and epigenetic regulatory pathways and by dissecting DNA sequence components involved in specifying targets. These experiments aim to unravel the crosstalk between epigenetic regulation and cell plasticity, the underlying molecular circuitry in pluripotent and unipotent cells and ultimately help to incorporate epigenetic regulation into current transcriptional regulatory models.
Summary
Differentiation events in mammalian development involve stable resetting of transcriptional programs, which entails changes in the epigenetic state of target sequences defined by modifications of DNA and bound nucleosomes. These recently identified epigenetic layers modulate DNA accessibility in a positive and negative manner and thus could make genetic readouts context-dependent and dynamic. The proposed project aims to quantify the epigenetic contribution to cellular differentiation as a key event in development. By applying parallel genomic approaches we will comprehensively define the epigenome and its plasticity during cellular commitment of pluripotent murine stem cells into defined terminally differentiated cells. We will focus on DNA methylation and its interplay with several histone modifications as a way to achieve stable gene silencing. The resulting global profiles will gain insights into targeting principles and generate statistical, predictive models of regulation. From these mechanistic models will be derived and tested by genetically interfering with genetic and epigenetic regulatory pathways and by dissecting DNA sequence components involved in specifying targets. These experiments aim to unravel the crosstalk between epigenetic regulation and cell plasticity, the underlying molecular circuitry in pluripotent and unipotent cells and ultimately help to incorporate epigenetic regulation into current transcriptional regulatory models.
Max ERC Funding
1 085 000 €
Duration
Start date: 2008-10-01, End date: 2013-09-30
Project acronym EPIRNAS
Project Small RNA Mediated Epigenetics in Vertebrates
Researcher (PI) René Ketting
Host Institution (HI) INSTITUT FUR MOLEKULARE BIOLOGIE GGMBH
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Since the discovery of RNAi small RNA molecules have been under intense study. They have been shown to impact many different processes, ranging from development to organ function and carcinogenesis. Recently, it has become clear that many distinct small RNA families exist. However, all act through a member of the well-conserved Argonaute family of proteins. I try to understand how specificity of the different Argonaute proteins is achieved, and I am particularly interested in Argonautes that may contribute to the epigenetic marking of genomic DNA in animals. My focus is on Argonaute function in the vertebrate germline, a tissue that is an especially intriguing system with regard to the resetting and establishment of epigenetic marks. As model system I use the zebrafish. Piwi proteins are Argonaute proteins that in vertebrates are specifically expressed in germ cells, and have been implicated in modifying chromatin structures. We demonstrated that zebrafish piwi is expressed in both the male and the female gonad and that loss of piwi results in loss of germ cells due to apoptosis. We have characterized small RNAs that bind to piwi (piRNAs) in both ovary and testis, and found that they play a role in the silencing of transposable elements. Furthermore, we have shown that the biogenesis of piRNAs differs markedly from that of other small RNAs like miRNAs. The experiments I propose address how Piwi proteins and piRNAs act in germ cells to ensure a functional germline and a stable propagation of intact chromatin over generations. First, I will address the biogenesis of piRNAs. Second, I will identify novel components of the Piwi pathway. Third, I will address the mode(s) of action of piRNAs. On all fronts a combination of genetics, molecular biology and biochemistry will be used.
Summary
Since the discovery of RNAi small RNA molecules have been under intense study. They have been shown to impact many different processes, ranging from development to organ function and carcinogenesis. Recently, it has become clear that many distinct small RNA families exist. However, all act through a member of the well-conserved Argonaute family of proteins. I try to understand how specificity of the different Argonaute proteins is achieved, and I am particularly interested in Argonautes that may contribute to the epigenetic marking of genomic DNA in animals. My focus is on Argonaute function in the vertebrate germline, a tissue that is an especially intriguing system with regard to the resetting and establishment of epigenetic marks. As model system I use the zebrafish. Piwi proteins are Argonaute proteins that in vertebrates are specifically expressed in germ cells, and have been implicated in modifying chromatin structures. We demonstrated that zebrafish piwi is expressed in both the male and the female gonad and that loss of piwi results in loss of germ cells due to apoptosis. We have characterized small RNAs that bind to piwi (piRNAs) in both ovary and testis, and found that they play a role in the silencing of transposable elements. Furthermore, we have shown that the biogenesis of piRNAs differs markedly from that of other small RNAs like miRNAs. The experiments I propose address how Piwi proteins and piRNAs act in germ cells to ensure a functional germline and a stable propagation of intact chromatin over generations. First, I will address the biogenesis of piRNAs. Second, I will identify novel components of the Piwi pathway. Third, I will address the mode(s) of action of piRNAs. On all fronts a combination of genetics, molecular biology and biochemistry will be used.
Max ERC Funding
970 000 €
Duration
Start date: 2008-08-01, End date: 2014-07-31
Project acronym ERNBPTC
Project Expression regulatory networks: beyond promoters and transcription control
Researcher (PI) Yitzhak Pilpel
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary "Gene expression in living cells is a most intricate molecular process, occurring in stages, each of which is regulated by a diversity of mechanisms. Among the various stages leading to gene expression, only transcription is relatively well understood, thanks to Genomics and bioinformatics. In contrast to the vast amounts of genome-wide data and a growing understanding of the structure of networks controlling transcription, we still lack quantitative, genome-wide knowledge of the mechanisms underlying regulation of mRNA degradation and translation. Among the unknowns are the identity of the regulators, their kinetic modes of action, and their means of interaction with the sequence features that make-up their targets; how these target combine to produce a higher level ""grammar"" is also unknown. An important part of the project is dedicated to generating genome-wide experimental data that will form the basis for quantitative and more comprehensive analysis of gene expression. Specifically, the primary objectives of our proposed research plan are: 1) to advance our understanding of the transcriptome, by deciphering the code regulating mRNA decay 2) to break the code which controls protein translation efficiency 3) to understand how mRNA degradation and translation efficiency determine noise in protein expression levels. The proposed strategy is based on an innovative combination of computational prediction, synthetic gene design, and genome-wide data acquisition, all culminating in extensive data analysis, mathematical modeling and focused experiments. This highly challenging, multidisciplinary project is likely to greatly enhance our knowledge of the various modes by which organisms regulate expression of their genomes, how these regulatory mechanisms are interrelated, how they generate precise response to environmental challenges and how they have evolved over time."
Summary
"Gene expression in living cells is a most intricate molecular process, occurring in stages, each of which is regulated by a diversity of mechanisms. Among the various stages leading to gene expression, only transcription is relatively well understood, thanks to Genomics and bioinformatics. In contrast to the vast amounts of genome-wide data and a growing understanding of the structure of networks controlling transcription, we still lack quantitative, genome-wide knowledge of the mechanisms underlying regulation of mRNA degradation and translation. Among the unknowns are the identity of the regulators, their kinetic modes of action, and their means of interaction with the sequence features that make-up their targets; how these target combine to produce a higher level ""grammar"" is also unknown. An important part of the project is dedicated to generating genome-wide experimental data that will form the basis for quantitative and more comprehensive analysis of gene expression. Specifically, the primary objectives of our proposed research plan are: 1) to advance our understanding of the transcriptome, by deciphering the code regulating mRNA decay 2) to break the code which controls protein translation efficiency 3) to understand how mRNA degradation and translation efficiency determine noise in protein expression levels. The proposed strategy is based on an innovative combination of computational prediction, synthetic gene design, and genome-wide data acquisition, all culminating in extensive data analysis, mathematical modeling and focused experiments. This highly challenging, multidisciplinary project is likely to greatly enhance our knowledge of the various modes by which organisms regulate expression of their genomes, how these regulatory mechanisms are interrelated, how they generate precise response to environmental challenges and how they have evolved over time."
Max ERC Funding
1 320 000 €
Duration
Start date: 2008-09-01, End date: 2013-08-31
Project acronym NCRNAX
Project Regulation and function of non-coding RNAs in epigenetic processes: the paradigm of X-chromosome inactivation
Researcher (PI) Claire Rougeulle
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary Some 150 years after the emergence of genetics, epigenetic mechanisms are increasingly understood to be fundamental players in phenotype transmission and development. In addition, epigenetic alterations are now linked to several human diseases including cancers. A common feature of many epigenetic phenomena, for which X-chromosome inactivation (XCI) is the paradigm, is the implication of non-coding RNAs (ncRNAs). Regulatory ncRNAs belong to 2 major classes: (i) long ncRNAs, which can be transcribed from a single strand as well as in the opposite orientation when they may overlap with either protein-coding or non-coding genes. Both sense (Xist) and antisense (Tsix) ncRNAs control the initiation of XCI; and (ii) short ncRNAs, such as si- or miRNAs, which interfere, through different pathways, with gene function. The aim of this project is to gain insights into the regulation and function of ncRNAs in the control of gene expression program, using XCI as a model system. We propose to combine molecular genetics, embryology and cell biology to (1) decipher the transcriptional control of Xist and the coordinate regulation of the Xist/Tsix sense/antisense tandem in relation to developmental programs; (2) functionally characterise a novel ncRNA on the X chromosome which nests several miRNAs and for which preliminary data suggest a role in XCI and (3) develop a system to extend our knowledge of the regulatory stages of XCI in human through the use of human embryonic stem cells. Our comprehensive analysis of the function and regulation of ncRNAs in XCI has important implications for our understanding of the numerous diseases associated with abnormal patterns of inactivation and is a critical prerequisite to any subsequent therapeutic approaches. This project is in absolute adequacy with the future “Epigenetic and Cell Fate “ host centre co-headed by Prs. Lalande and Viegas-Pequignot, a large-scale initiative expected to strengthen French and European research in Epigenetics.
Summary
Some 150 years after the emergence of genetics, epigenetic mechanisms are increasingly understood to be fundamental players in phenotype transmission and development. In addition, epigenetic alterations are now linked to several human diseases including cancers. A common feature of many epigenetic phenomena, for which X-chromosome inactivation (XCI) is the paradigm, is the implication of non-coding RNAs (ncRNAs). Regulatory ncRNAs belong to 2 major classes: (i) long ncRNAs, which can be transcribed from a single strand as well as in the opposite orientation when they may overlap with either protein-coding or non-coding genes. Both sense (Xist) and antisense (Tsix) ncRNAs control the initiation of XCI; and (ii) short ncRNAs, such as si- or miRNAs, which interfere, through different pathways, with gene function. The aim of this project is to gain insights into the regulation and function of ncRNAs in the control of gene expression program, using XCI as a model system. We propose to combine molecular genetics, embryology and cell biology to (1) decipher the transcriptional control of Xist and the coordinate regulation of the Xist/Tsix sense/antisense tandem in relation to developmental programs; (2) functionally characterise a novel ncRNA on the X chromosome which nests several miRNAs and for which preliminary data suggest a role in XCI and (3) develop a system to extend our knowledge of the regulatory stages of XCI in human through the use of human embryonic stem cells. Our comprehensive analysis of the function and regulation of ncRNAs in XCI has important implications for our understanding of the numerous diseases associated with abnormal patterns of inactivation and is a critical prerequisite to any subsequent therapeutic approaches. This project is in absolute adequacy with the future “Epigenetic and Cell Fate “ host centre co-headed by Prs. Lalande and Viegas-Pequignot, a large-scale initiative expected to strengthen French and European research in Epigenetics.
Max ERC Funding
1 220 000 €
Duration
Start date: 2009-04-01, End date: 2014-03-31
