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 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 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
Project acronym PROTMOD
Project Dynamics and stability of covalent protein modifications
Researcher (PI) Robert Schneider
Host Institution (HI) CENTRE EUROPEEN DE RECHERCHE EN BIOLOGIE ET MEDECINE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary "One of the major goals of post-genomic biological research is to understand the molecular basis and physiological role of covalent protein modifications. Post-transcriptional modifications can regulate protein interactions and/or stability and thus trigger particular downstream responses. A major challenge is to understand how modifications of histone proteins are translated into changes in gene expression and chromatin structure and how they regulate genome function. However, the significance of studying protein modifications extends beyond the field of chromatin research, because changes in the modification pattern are likely to affect many -if not all- biological processes. This proposal is designed to study and functionally characterise modifications of histones. The goals of this proposal are: A) Determining the role of linker H1 modifications and variants in epigenetic regulation of gene expression. This will enable us to expand the ""histone"" code to the next higher level of chromatin organisation. B) To identify yet uncharacterised sites or new types of histone modifications. This will be the basis for determining the biological function of these modifications. Altogether this will lead us to decipher the role of covalent protein modifications in regulation of gene expression and how they are linked into biological networks . These projects will significantly expand the scope of my ongoing research and will only be possible with additional funding, which will allow me to establish cutting edge technology, additional in vivo model systems and new interdisciplinary collaborations."
Summary
"One of the major goals of post-genomic biological research is to understand the molecular basis and physiological role of covalent protein modifications. Post-transcriptional modifications can regulate protein interactions and/or stability and thus trigger particular downstream responses. A major challenge is to understand how modifications of histone proteins are translated into changes in gene expression and chromatin structure and how they regulate genome function. However, the significance of studying protein modifications extends beyond the field of chromatin research, because changes in the modification pattern are likely to affect many -if not all- biological processes. This proposal is designed to study and functionally characterise modifications of histones. The goals of this proposal are: A) Determining the role of linker H1 modifications and variants in epigenetic regulation of gene expression. This will enable us to expand the ""histone"" code to the next higher level of chromatin organisation. B) To identify yet uncharacterised sites or new types of histone modifications. This will be the basis for determining the biological function of these modifications. Altogether this will lead us to decipher the role of covalent protein modifications in regulation of gene expression and how they are linked into biological networks . These projects will significantly expand the scope of my ongoing research and will only be possible with additional funding, which will allow me to establish cutting edge technology, additional in vivo model systems and new interdisciplinary collaborations."
Max ERC Funding
1 239 400 €
Duration
Start date: 2008-09-01, End date: 2014-08-31
Project acronym RANK
Project The Formation and Visualisation of the Social and Political Order of Princes in late Medieval Europe. A Comparative Study between the Empire and England
Researcher (PI) Jörg Henning Peltzer
Host Institution (HI) RUPRECHT-KARLS-UNIVERSITAET HEIDELBERG
Call Details Starting Grant (StG), SH5, ERC-2007-StG
Summary This project examines the formation and differentiation of princely elites in pre-modern European rank societies. The project concentrates on the late Middle Ages (1200–1500), a key period in these processes, with geographic focus on the Empire and England. In both polities new princely elites emerged during this period. Yet, they did so in the context of the establishment of two different monarchical principles, the elective kingship in the Empire and the hereditary kingship in England. In the Empire, the electoral princes became a distinctive group and constituted themselves as the pillars of the imperium. In England, the title of duke appears to have been introduced to distinguish members of the royal family from other magnates. In examining these complex social and political processes in both polities the project contributes to establish a typology of different ways of constructing societies in pre-modern Europe using an interdisciplinary, comparative approach. The project combines history, architectural and art history, archaeology and semiotics to analyse princely actions, princely architecture and heraldry. In so doing we will endeavour to determine the strategies developed and deployed by princes in late medieval Europe to represent and improve their rank and thus their significance. The comparison sheds light on several key issues such as whether the emperorship, unique in Europe, enabled the development of a king-like position for (electoral) princes, and how in different political contexts the position of the magnates in relation to each other and the king was communicated and perpetuated. This project breaks new ground on several frontiers. Interconnecting different disciplines, it crosses existing subject boundaries and thus opens up new ways of fruitful cooperation. By comparing the Empire with England the project also transgresses the traditional boundaries of national history, thus helping to establish a European perspective in medieval studies.
Summary
This project examines the formation and differentiation of princely elites in pre-modern European rank societies. The project concentrates on the late Middle Ages (1200–1500), a key period in these processes, with geographic focus on the Empire and England. In both polities new princely elites emerged during this period. Yet, they did so in the context of the establishment of two different monarchical principles, the elective kingship in the Empire and the hereditary kingship in England. In the Empire, the electoral princes became a distinctive group and constituted themselves as the pillars of the imperium. In England, the title of duke appears to have been introduced to distinguish members of the royal family from other magnates. In examining these complex social and political processes in both polities the project contributes to establish a typology of different ways of constructing societies in pre-modern Europe using an interdisciplinary, comparative approach. The project combines history, architectural and art history, archaeology and semiotics to analyse princely actions, princely architecture and heraldry. In so doing we will endeavour to determine the strategies developed and deployed by princes in late medieval Europe to represent and improve their rank and thus their significance. The comparison sheds light on several key issues such as whether the emperorship, unique in Europe, enabled the development of a king-like position for (electoral) princes, and how in different political contexts the position of the magnates in relation to each other and the king was communicated and perpetuated. This project breaks new ground on several frontiers. Interconnecting different disciplines, it crosses existing subject boundaries and thus opens up new ways of fruitful cooperation. By comparing the Empire with England the project also transgresses the traditional boundaries of national history, thus helping to establish a European perspective in medieval studies.
Max ERC Funding
900 000 €
Duration
Start date: 2008-10-01, End date: 2014-09-30
Project acronym RNAIEPIMOD
Project RNA and Epigenetics: RNAi-Driven Chromatin Modifications
Researcher (PI) André Verdel
Host Institution (HI) INSTITUT NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE
Call Details Starting Grant (StG), LS2, ERC-2007-StG
Summary RNA interference (RNAi) mediates chromatin modifications in fungi, plants, drosophila and vertebrates. In the fission yeast Schizosaccharomyces pombe, where the molecular mechanisms are the most detailed, it is believed that small interfering RNAs (siRNAs) guide the RNA-Induced Transcriptional Silencing (RITS) complex to specific chromatin regions to trigger formation of heterochromatin. Although it is clear that siRNAs are required for RITS localization to chromatin, important events of RITS siRNA-dependent recruitment remain to be elucidated. Additionally, critical aspects of the following RITS-driven heterochromatin formation mechanism need to be clarified. Genetic data indicate that among proteins required for assembly of heterochromatin some act very early in this process to the point that they should interact directly or indirectly with RITS. However, no physical connection between RITS and these enzymes has yet been found. This project proposes to address these fundamental aspects of RNAi-mediated heterochromatin assembly in S.pombe, by coupling interdisciplinary and innovative approaches to classical protein affinity purifications, yeast molecular genetics and chromatin techniques. The first part of the project will concentrate on the characterization of an unprecedented physical connection between RITS and a chromatin-modifying activity. In parallel, we propose to develop two complementary approaches to identify new proteins that physically and/or genetically interact with RITS. Finally, thanks to a UV light-induced crosslinking technology, we intend to study RITS recruitment to chromatin by analyzing its direct interaction with nucleic acids both in vitro and in vivo. As the control of chromatin structure by RNAi is evolutionary conserved, our studies have the potential to bring general insights into how RNAi-based chromatin modifications take place and are regulated in the kingdom of eukaryotes.
Summary
RNA interference (RNAi) mediates chromatin modifications in fungi, plants, drosophila and vertebrates. In the fission yeast Schizosaccharomyces pombe, where the molecular mechanisms are the most detailed, it is believed that small interfering RNAs (siRNAs) guide the RNA-Induced Transcriptional Silencing (RITS) complex to specific chromatin regions to trigger formation of heterochromatin. Although it is clear that siRNAs are required for RITS localization to chromatin, important events of RITS siRNA-dependent recruitment remain to be elucidated. Additionally, critical aspects of the following RITS-driven heterochromatin formation mechanism need to be clarified. Genetic data indicate that among proteins required for assembly of heterochromatin some act very early in this process to the point that they should interact directly or indirectly with RITS. However, no physical connection between RITS and these enzymes has yet been found. This project proposes to address these fundamental aspects of RNAi-mediated heterochromatin assembly in S.pombe, by coupling interdisciplinary and innovative approaches to classical protein affinity purifications, yeast molecular genetics and chromatin techniques. The first part of the project will concentrate on the characterization of an unprecedented physical connection between RITS and a chromatin-modifying activity. In parallel, we propose to develop two complementary approaches to identify new proteins that physically and/or genetically interact with RITS. Finally, thanks to a UV light-induced crosslinking technology, we intend to study RITS recruitment to chromatin by analyzing its direct interaction with nucleic acids both in vitro and in vivo. As the control of chromatin structure by RNAi is evolutionary conserved, our studies have the potential to bring general insights into how RNAi-based chromatin modifications take place and are regulated in the kingdom of eukaryotes.
Max ERC Funding
904 940 €
Duration
Start date: 2009-01-01, End date: 2013-12-31
Project acronym SIANHE
Project Stable isotope investigations on the adaptations of Neolithic husbandry to the diverse climatic and environmental settings of Eastern, Central and Western Europe
Researcher (PI) Marie Balasse
Host Institution (HI) MUSEUM NATIONAL D'HISTOIRE NATURELLE
Call Details Starting Grant (StG), SH5, ERC-2007-StG
Summary Twenty-first century European husbandry results from thousand-year-old experiences. This project aims at giving a historical dimension to the growing questioning on present day herding practices among European consumers. Sheep, goat, cattle and pig were domesticated ca. 8500 cal. BC in the eastern Taurus. From there they spread to most of the Near East and entered Europe at the turn of the 7th millennium BC. They reached the North-western Europe coasts by the beginning of the 5th millennium and colonised the British islands during the 4th and 3rd millennia BC. Whereas domestication of European wild boar could have occurred, European aurochs did not contribute significantly to cattle populations. Sheep and goat do not have wild ancestors in Europe. Most of these animals actually stem from populations transferred from the Near East. The spread of domestic species outside the natural range of occurrence of their wild counterparts, their keeping in environmental settings different from their natural ecological niches, and the will to stimulate milk production in bovines and ovicaprines, imply some modifications in dietary and reproduction behaviours of domestic animals. Neolithic herders developed zootechnical skills to insure survival of their stock and the adaptation of their production strategies to new environments. The objective of this project is to evaluate the environmental and physiological constraints on the adaptation of stock keeping in Europe, and to determine to what extant Neolithic herders could modulate the biological system with technical choices. Landscape use, seasonal foddering, seasonality of birth and duration of lactation will be addressed using stable isotope analysis on animal bone and teeth. The animals stress condition will be assessed through analysis of enamel hypoplasia. The project includes Neolithic sites from Caucasia, Eastern, Central and Western Europe. It will necessitate methodological developments on modern reference skeletons.
Summary
Twenty-first century European husbandry results from thousand-year-old experiences. This project aims at giving a historical dimension to the growing questioning on present day herding practices among European consumers. Sheep, goat, cattle and pig were domesticated ca. 8500 cal. BC in the eastern Taurus. From there they spread to most of the Near East and entered Europe at the turn of the 7th millennium BC. They reached the North-western Europe coasts by the beginning of the 5th millennium and colonised the British islands during the 4th and 3rd millennia BC. Whereas domestication of European wild boar could have occurred, European aurochs did not contribute significantly to cattle populations. Sheep and goat do not have wild ancestors in Europe. Most of these animals actually stem from populations transferred from the Near East. The spread of domestic species outside the natural range of occurrence of their wild counterparts, their keeping in environmental settings different from their natural ecological niches, and the will to stimulate milk production in bovines and ovicaprines, imply some modifications in dietary and reproduction behaviours of domestic animals. Neolithic herders developed zootechnical skills to insure survival of their stock and the adaptation of their production strategies to new environments. The objective of this project is to evaluate the environmental and physiological constraints on the adaptation of stock keeping in Europe, and to determine to what extant Neolithic herders could modulate the biological system with technical choices. Landscape use, seasonal foddering, seasonality of birth and duration of lactation will be addressed using stable isotope analysis on animal bone and teeth. The animals stress condition will be assessed through analysis of enamel hypoplasia. The project includes Neolithic sites from Caucasia, Eastern, Central and Western Europe. It will necessitate methodological developments on modern reference skeletons.
Max ERC Funding
883 802 €
Duration
Start date: 2008-10-01, End date: 2014-02-28
