Project acronym ACTINONSRF
Project MAL: an actin-regulated SRF transcriptional coactivator
Researcher (PI) Richard Treisman
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Call Details Advanced Grant (AdG), LS1, ERC-2010-AdG_20100317
Summary MAL: an actin-regulated SRF transcriptional coactivator
Recent years have seen a revitalised interest in the role of actin in nuclear processes, but the molecular mechanisms involved remain largely unexplored. We will elucidate the molecular basis for the actin-based control of the SRF transcriptional coactivator, MAL. SRF controls transcription through two families of coactivators, the actin-binding MRTFs (MAL, Mkl2), which couple its activity to cytoskeletal dynamics, and the ERK-regulated TCFs (Elk-1, SAP-1, Net). MAL subcellular localisation and transcriptional activity responds to signal-induced changes in G-actin concentration, which are sensed by its actin-binding N-terminal RPEL domain. Members of a second family of RPEL proteins, the Phactrs, also exhibit actin-regulated nucleocytoplasmic shuttling. The proposal addresses the following novel features of actin biology:
¿ Actin as a transcriptional regulator
¿ Actin as a signalling molecule
¿ Actin-binding proteins as targets for regulation by actin, rather than regulators of actin function
We will analyse the sequences and proteins involved in actin-regulated nucleocytoplasmic shuttling, using structural biology and biochemistry to analyse its control by changes in actin-RPEL domain interactions. We will characterise the dynamics of shuttling, and develop reporters for changes in actin-MAL interaction for analysis of pathway activation in vivo. We will identify genes controlling MAL itself, and the balance between the nuclear and cytoplasmic actin pools. The mechanism by which actin represses transcriptional activation by MAL in the nucleus, and its relation to MAL phosphorylation, will be elucidated. Finally, we will map MRTF and TCF cofactor recruitment to SRF targets on a genome-wide scale, and identify the steps in transcription controlled by actin-MAL interaction.
Summary
MAL: an actin-regulated SRF transcriptional coactivator
Recent years have seen a revitalised interest in the role of actin in nuclear processes, but the molecular mechanisms involved remain largely unexplored. We will elucidate the molecular basis for the actin-based control of the SRF transcriptional coactivator, MAL. SRF controls transcription through two families of coactivators, the actin-binding MRTFs (MAL, Mkl2), which couple its activity to cytoskeletal dynamics, and the ERK-regulated TCFs (Elk-1, SAP-1, Net). MAL subcellular localisation and transcriptional activity responds to signal-induced changes in G-actin concentration, which are sensed by its actin-binding N-terminal RPEL domain. Members of a second family of RPEL proteins, the Phactrs, also exhibit actin-regulated nucleocytoplasmic shuttling. The proposal addresses the following novel features of actin biology:
¿ Actin as a transcriptional regulator
¿ Actin as a signalling molecule
¿ Actin-binding proteins as targets for regulation by actin, rather than regulators of actin function
We will analyse the sequences and proteins involved in actin-regulated nucleocytoplasmic shuttling, using structural biology and biochemistry to analyse its control by changes in actin-RPEL domain interactions. We will characterise the dynamics of shuttling, and develop reporters for changes in actin-MAL interaction for analysis of pathway activation in vivo. We will identify genes controlling MAL itself, and the balance between the nuclear and cytoplasmic actin pools. The mechanism by which actin represses transcriptional activation by MAL in the nucleus, and its relation to MAL phosphorylation, will be elucidated. Finally, we will map MRTF and TCF cofactor recruitment to SRF targets on a genome-wide scale, and identify the steps in transcription controlled by actin-MAL interaction.
Max ERC Funding
1 889 995 €
Duration
Start date: 2011-10-01, End date: 2017-09-30
Project acronym ARCID
Project The Role of Arl Proteins in Retinal and other Ciliary Diseases
Researcher (PI) Alfred Wittinghofer
Host Institution (HI) Klinik Max Planck Institut für Psychiatrie
Call Details Advanced Grant (AdG), LS1, ERC-2010-AdG_20100317
Summary Arl (Arf-like) proteins, GTP-binding proteins of the Ras superfamily, are molecular switches that cycle between a GDP-bound inactive and GTP-bound active state. There are 16 members of the Arl subfamily in the human genome whose basic mechanistic function is unknown. The interactome of Arl2/3 includes proteins involved in retinopathies and other ciliary diseases such as Leber¿s Congenital Amaurosis (LCA) and kidney diseases such as nephronophthisis. Arl6 has been found mutated in Bardet Biedl Syndrome, another pleiotropic ciliary disease. In the proposed interdisciplinary project I want to explore the function of the protein network of Arl2/3 and Arl6 by a combination of biochemical, biophysical and structural methods and use the knowledge obtained to probe their function in live cells. As with other subfamily proteins of the Ras superfamily which have been found to mediate similar biological functions I want to derive a basic understanding of the function of Arl proteins and how it relates to the development and function of the ciliary organelle and how they contribute to ciliary diseases. The molecules in the focus of the project are: the GTP-binding proteins Arl2, 3, 6; RP2, an Arl3GAP mutated in Retinitis pigmentosa; Regulators of Arl2 and 3; PDE¿ and HRG4, effectors of Arl2/3, which bind lipidated proteins; RPGR, mutated in Retinitis pigmentosa, an interactor of PDE¿; RPGRIP and RPGRIPL, interactors of RPGR mutated in LCA and other ciliopathies; Nephrocystin, mutated in nephronophthisis, an interactor of RPGRIP and Arl6, mutated in Bardet Biedl Syndrome, and the BBS complex. The working hypothesis is that Arl protein network(s) mediate ciliary transport processes and that the GTP switch cycle of Arl proteins is an important element of regulation of these processes.
Summary
Arl (Arf-like) proteins, GTP-binding proteins of the Ras superfamily, are molecular switches that cycle between a GDP-bound inactive and GTP-bound active state. There are 16 members of the Arl subfamily in the human genome whose basic mechanistic function is unknown. The interactome of Arl2/3 includes proteins involved in retinopathies and other ciliary diseases such as Leber¿s Congenital Amaurosis (LCA) and kidney diseases such as nephronophthisis. Arl6 has been found mutated in Bardet Biedl Syndrome, another pleiotropic ciliary disease. In the proposed interdisciplinary project I want to explore the function of the protein network of Arl2/3 and Arl6 by a combination of biochemical, biophysical and structural methods and use the knowledge obtained to probe their function in live cells. As with other subfamily proteins of the Ras superfamily which have been found to mediate similar biological functions I want to derive a basic understanding of the function of Arl proteins and how it relates to the development and function of the ciliary organelle and how they contribute to ciliary diseases. The molecules in the focus of the project are: the GTP-binding proteins Arl2, 3, 6; RP2, an Arl3GAP mutated in Retinitis pigmentosa; Regulators of Arl2 and 3; PDE¿ and HRG4, effectors of Arl2/3, which bind lipidated proteins; RPGR, mutated in Retinitis pigmentosa, an interactor of PDE¿; RPGRIP and RPGRIPL, interactors of RPGR mutated in LCA and other ciliopathies; Nephrocystin, mutated in nephronophthisis, an interactor of RPGRIP and Arl6, mutated in Bardet Biedl Syndrome, and the BBS complex. The working hypothesis is that Arl protein network(s) mediate ciliary transport processes and that the GTP switch cycle of Arl proteins is an important element of regulation of these processes.
Max ERC Funding
2 434 400 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym CIRCATRANS
Project Control of mouse metabolism by circadian clock-coordinated mRNA translation
Researcher (PI) Frédéric Bruno Martin Gachon
Host Institution (HI) NESTEC SA
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
Summary
The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
Max ERC Funding
1 475 831 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym CRIPTON
Project Role of ncRNAs in Chromatin and Transcription
Researcher (PI) Tony Kouzarides
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS1, ERC-2010-AdG_20100317
Summary The human genome is highly transcribed, with over 90% of sequences contributing to the production of RNA. The function of the vast majority of these RNAs is unknown. Evidence over many years has revealed that transcription factors and chromatin regulators are associated with a variety of non-coding (nc)RNAs, but their function remains largely unknown. There are a few cases where a role has been ascribed for ncRNAs in transcription, but no clear mechanistic insight has been defined yet. We predict that many of the newly identified ncRNAs emanating from the genome will play a role in transcriptional processes. We intend to identify and characterise such ncRNAs. This will take place in two phases. In the first phase we will use biochemical approaches to identify ncRNAs involved in the regulation of chromatin and transcription. Our investigations will focus on proteins leading to the induction of pluripotency and oncogenesis. ncRNAs associated with such proteins will be identified using targeted screens. In the second phase, the importance of these RNAs in determining pluripotency and oncogenesis will be analysed. In addition, a variety of molecular approaches will be used to investigate the mechanism by which these ncRNAs regulate the function of the proteins or complexes they associate with. One particular hypothesis we will explore is that such ncRNAs play a role in guiding proteins to DNA sequences, via the formation of RNA/DNA triplexes. This concerted and focused analysis will provide mechanistic insights into the functions of ncRNAs in transcriptional regulation and validate their role in key biological processes. The identification of such new ncRNA-regulated pathways may open up new avenues for therapeutic intervention.
Summary
The human genome is highly transcribed, with over 90% of sequences contributing to the production of RNA. The function of the vast majority of these RNAs is unknown. Evidence over many years has revealed that transcription factors and chromatin regulators are associated with a variety of non-coding (nc)RNAs, but their function remains largely unknown. There are a few cases where a role has been ascribed for ncRNAs in transcription, but no clear mechanistic insight has been defined yet. We predict that many of the newly identified ncRNAs emanating from the genome will play a role in transcriptional processes. We intend to identify and characterise such ncRNAs. This will take place in two phases. In the first phase we will use biochemical approaches to identify ncRNAs involved in the regulation of chromatin and transcription. Our investigations will focus on proteins leading to the induction of pluripotency and oncogenesis. ncRNAs associated with such proteins will be identified using targeted screens. In the second phase, the importance of these RNAs in determining pluripotency and oncogenesis will be analysed. In addition, a variety of molecular approaches will be used to investigate the mechanism by which these ncRNAs regulate the function of the proteins or complexes they associate with. One particular hypothesis we will explore is that such ncRNAs play a role in guiding proteins to DNA sequences, via the formation of RNA/DNA triplexes. This concerted and focused analysis will provide mechanistic insights into the functions of ncRNAs in transcriptional regulation and validate their role in key biological processes. The identification of such new ncRNA-regulated pathways may open up new avenues for therapeutic intervention.
Max ERC Funding
2 141 470 €
Duration
Start date: 2011-05-01, End date: 2017-04-30
Project acronym D-END
Project Telomeres: from the DNA end replication problem to the control of cell proliferation
Researcher (PI) Maria Teresa Teixeira Fernandes Bernardo
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary Linear chromosomes of eukaryotes end with telomeres that ensure their stability. Because of the inability of semi-conservative DNA replication machinery to fully replicate DNA ends, telomeres require dedicated mechanisms to be duplicated and their length is eroded at each cell division. For this reason, telomeres constitute molecular clocks that determine cell proliferation potential in eukaryotes. Strikingly, we have shown recently that it is the shortest telomere in the cell that determines the onset of replicative senescence. This project aims a complete and detailed dissection of the in vivo DNA-end replication problem and the deep understanding of its impact for cell division capability. Specifically my goals are (1) the determination of the exact structures that result from the replication of DNA extremities, (2) the examination of the activities operating at the shortest telomere that triggers replicative senescence and (3) the investigation of the correspondence between telomere molecular structure and cell proliferation state at individual cell scale. To achieve this, I will undertake in Saccharomyces cerevisiae original and innovative single-molecule and single-cell approaches, that, in combination with genome-wide screens and sophisticated cellular settings, will allow to track and challenge a specified telomere of defined length. I anticipate that this work will lead to an in-depth understanding of how telomeres are replicated and how they enable the control of cell proliferation in eukaryotic cells, a matter at the intersection of the fundamentals of molecular genetics, cell biology of aging and oncology.
Summary
Linear chromosomes of eukaryotes end with telomeres that ensure their stability. Because of the inability of semi-conservative DNA replication machinery to fully replicate DNA ends, telomeres require dedicated mechanisms to be duplicated and their length is eroded at each cell division. For this reason, telomeres constitute molecular clocks that determine cell proliferation potential in eukaryotes. Strikingly, we have shown recently that it is the shortest telomere in the cell that determines the onset of replicative senescence. This project aims a complete and detailed dissection of the in vivo DNA-end replication problem and the deep understanding of its impact for cell division capability. Specifically my goals are (1) the determination of the exact structures that result from the replication of DNA extremities, (2) the examination of the activities operating at the shortest telomere that triggers replicative senescence and (3) the investigation of the correspondence between telomere molecular structure and cell proliferation state at individual cell scale. To achieve this, I will undertake in Saccharomyces cerevisiae original and innovative single-molecule and single-cell approaches, that, in combination with genome-wide screens and sophisticated cellular settings, will allow to track and challenge a specified telomere of defined length. I anticipate that this work will lead to an in-depth understanding of how telomeres are replicated and how they enable the control of cell proliferation in eukaryotic cells, a matter at the intersection of the fundamentals of molecular genetics, cell biology of aging and oncology.
Max ERC Funding
1 498 504 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym DDRREAM
Project DNA-Damage responses: Regulation and mechanisms
Researcher (PI) Stephen Philip Jackson
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARSOF THE UNIVERSITY OF CAMBRIDGE
Call Details Advanced Grant (AdG), LS1, ERC-2010-AdG_20100317
Summary The prime objective for every life form is to deliver its genetic material, intact, to the next generation. Each human cell receives tens-of-thousands of DNA lesions per day. These lesions can block genome replication and transcription, and if not repaired or repaired incorrectly, they lead to mutations or wider genome aberrations that threaten cell viability. To counter such threats, life has evolved the DNA-damage response (DDR), to detect DNA damage, signal its presence and mediate its repair. DDR events impact on many cellular processes and, crucially, prevent diverse human diseases that include cancer, neurodegenerative diseases, immune-deficiencies and premature ageing. While much progress has been made in identifying DDR proteins, much remains to be learned about the molecular and cellular functions that they control. Furthermore, the frequent reporting of new DDR proteins in the literature suggests that many others await identification. The main goals for the proposed research are to: identify important new DDR-proteins and DDR-modulators, particularly those responding to DNA double-strand breaks (DSBs); provide mechanistic insights into how these proteins function; and determine how DDR events are affected by chromatin structure, by molecular chaperones and components of the Ubiquitin and Sumo systems. To achieve these ends, we will use molecular biology, biochemical, cell-biology and molecular genetics approaches, including synthetic-lethal and phenotypic-suppression screening methods in human cells and in the nematode worm. This work will not only be of academic importance, but will also indicate how DDR dysfunction can cause human disease and how such diseases might be better diagnosed and treated.
Summary
The prime objective for every life form is to deliver its genetic material, intact, to the next generation. Each human cell receives tens-of-thousands of DNA lesions per day. These lesions can block genome replication and transcription, and if not repaired or repaired incorrectly, they lead to mutations or wider genome aberrations that threaten cell viability. To counter such threats, life has evolved the DNA-damage response (DDR), to detect DNA damage, signal its presence and mediate its repair. DDR events impact on many cellular processes and, crucially, prevent diverse human diseases that include cancer, neurodegenerative diseases, immune-deficiencies and premature ageing. While much progress has been made in identifying DDR proteins, much remains to be learned about the molecular and cellular functions that they control. Furthermore, the frequent reporting of new DDR proteins in the literature suggests that many others await identification. The main goals for the proposed research are to: identify important new DDR-proteins and DDR-modulators, particularly those responding to DNA double-strand breaks (DSBs); provide mechanistic insights into how these proteins function; and determine how DDR events are affected by chromatin structure, by molecular chaperones and components of the Ubiquitin and Sumo systems. To achieve these ends, we will use molecular biology, biochemical, cell-biology and molecular genetics approaches, including synthetic-lethal and phenotypic-suppression screening methods in human cells and in the nematode worm. This work will not only be of academic importance, but will also indicate how DDR dysfunction can cause human disease and how such diseases might be better diagnosed and treated.
Max ERC Funding
2 482 492 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym DISENTANGLE
Project Untangling the Bacterial Chromosome: Condensin's Role in Sister Chromosome Separation and its Mechanisms
Researcher (PI) Stephan Gruber
Host Institution (HI) Klinik Max Planck Institut für Psychiatrie
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary A prerequisite for chromosome segregation in all living organisms is the topological unlinking of sister DNA molecules, called DNA decatenation. Decatenation is performed by DNA topoisomerases that work by transiently breaking strand(s) in one DNA double helix and passing another double helix through the temporarily created gate. How DNA topoisomerases manage to recognize linkages between sister DNA molecules and how they promote decatenation of sister chromatids (but not catenation) is still largely unknown.
The driving hypothesis of this project is that condensin promotes chromosome decatenation by guiding the unlinking activity of DNA topoisomerases. Condensin is a member of the family of SMC (Structural Maintenance of Chromosomes) protein complexes that is conserved from bacteria to humans. It forms large, ring-like structures that bind to and organize chromosomes. Efficient separation of sister chromosomes in the bacterium B. subtilis depends on the condensin complex. However, so far the precise role of condensin in chromosome segregation and its mechanisms are unclear.
To test our hypothesis, we will establish a minichromosome in bacteria that segregates in a condensin-dependent manner and measure its decatenation in vivo in the presence and absence of condensin. We will investigate the mechanism by which condensin organizes DNA within the (mini-)chromosome using techniques like chromosome conformation capture (3C) and electron microscopy. Finally, we will attempt to reconstitute for the first time the entrapment of DNA double helices by ring-like SMC protein complexes using purified components. Our results will be pivotal for understanding the action of SMC proteins in general with important implications in the separation and segregation of chromosomes in bacteria, the shaping of mitotic chromosomes and the resolution of sister chromatids during mitosis in eukaryotes.
Summary
A prerequisite for chromosome segregation in all living organisms is the topological unlinking of sister DNA molecules, called DNA decatenation. Decatenation is performed by DNA topoisomerases that work by transiently breaking strand(s) in one DNA double helix and passing another double helix through the temporarily created gate. How DNA topoisomerases manage to recognize linkages between sister DNA molecules and how they promote decatenation of sister chromatids (but not catenation) is still largely unknown.
The driving hypothesis of this project is that condensin promotes chromosome decatenation by guiding the unlinking activity of DNA topoisomerases. Condensin is a member of the family of SMC (Structural Maintenance of Chromosomes) protein complexes that is conserved from bacteria to humans. It forms large, ring-like structures that bind to and organize chromosomes. Efficient separation of sister chromosomes in the bacterium B. subtilis depends on the condensin complex. However, so far the precise role of condensin in chromosome segregation and its mechanisms are unclear.
To test our hypothesis, we will establish a minichromosome in bacteria that segregates in a condensin-dependent manner and measure its decatenation in vivo in the presence and absence of condensin. We will investigate the mechanism by which condensin organizes DNA within the (mini-)chromosome using techniques like chromosome conformation capture (3C) and electron microscopy. Finally, we will attempt to reconstitute for the first time the entrapment of DNA double helices by ring-like SMC protein complexes using purified components. Our results will be pivotal for understanding the action of SMC proteins in general with important implications in the separation and segregation of chromosomes in bacteria, the shaping of mitotic chromosomes and the resolution of sister chromatids during mitosis in eukaryotes.
Max ERC Funding
1 376 734 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym DNA ORIGAMI DEVICES
Project Single-molecule studies of protein-protein and protein-DNA interactions, enabled by DNA origami
Researcher (PI) Hendrik Dietz
Host Institution (HI) TECHNISCHE UNIVERSITAET MUENCHEN
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary Adhesive interactions between macromolecules are ubiquitously found in biology. Regulatory processes in biology depend on temporary physical inter-biomolecular interactions whose strengths are regulated by the internal state of the cell. Obtaining quantitative insight the dynamic strength of interactions between biomolecules has remained a difficult task. Single-molecule approaches can provide detailed insight into intra-molecular interactions in biomolecules. Yet, protein-protein and protein-DNA interactions have remained largely inaccessible. We propose to enable the single-molecule study of protein and protein-DNA interactions by taking advantage of the fine positional control afforded by DNA origami to overcome critical experimental challenges. As a first case study we plan to employ the DNA origami devices to study the single-molecule mechanics protein-protein and protein-DNA interactions that are relevant in the regulation of the galactose metabolism in yeast. We also seek to take steps towards a high-throughput single-molecule protein-DNA and protein-protein interaction assay to open access to a quantitative and combinatorial study of many different inter-macromolecular interactions, as well as to study the effects exerted by additional inhibiting or activating ligands. The proposed project will open up novel opportunities for a systematic study of macromolecular interactions in biology and is likely to deepen our understanding of regulatory processes in biology. Lessons that will be learned may suggest new ways to the rational design or identification of compounds that can prevent disease-causing interactions.
Summary
Adhesive interactions between macromolecules are ubiquitously found in biology. Regulatory processes in biology depend on temporary physical inter-biomolecular interactions whose strengths are regulated by the internal state of the cell. Obtaining quantitative insight the dynamic strength of interactions between biomolecules has remained a difficult task. Single-molecule approaches can provide detailed insight into intra-molecular interactions in biomolecules. Yet, protein-protein and protein-DNA interactions have remained largely inaccessible. We propose to enable the single-molecule study of protein and protein-DNA interactions by taking advantage of the fine positional control afforded by DNA origami to overcome critical experimental challenges. As a first case study we plan to employ the DNA origami devices to study the single-molecule mechanics protein-protein and protein-DNA interactions that are relevant in the regulation of the galactose metabolism in yeast. We also seek to take steps towards a high-throughput single-molecule protein-DNA and protein-protein interaction assay to open access to a quantitative and combinatorial study of many different inter-macromolecular interactions, as well as to study the effects exerted by additional inhibiting or activating ligands. The proposed project will open up novel opportunities for a systematic study of macromolecular interactions in biology and is likely to deepen our understanding of regulatory processes in biology. Lessons that will be learned may suggest new ways to the rational design or identification of compounds that can prevent disease-causing interactions.
Max ERC Funding
1 494 216 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym DNAMETRY
Project DNA based nanometry: Exploring chromatin structure and molecular motors
Researcher (PI) Ralf Seidel
Host Institution (HI) UNIVERSITAET LEIPZIG
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary DNA metabolism is governed by a delicate balance between compacting the stored genetic information while simultaneously ensuring a highly dynamically access to it. This interdisciplinary project aims (i) to understand the mechanics and dynamics of chromatin as well as the mechanism of enzymes involved in DNA metabolism on a molecular level and (ii) to develop new nanometric tools based on optical methods and 3D DNA nanostructures that allow addressing new experimental questions. Within the research project novel nanoscopic detection assays based on the combination of magnetic tweezers and optical methods shall be developed, such as ultra-fast torque spectroscopy and combined FRET-force spectroscopy. Our single-molecule assays shall be applied to study the material properties of self-assembled 3D DNA nanostructures, which shall then be used to set up improved high resolution single-molecule assays. These technological improvements will become key to obtain insight into structure and dynamics of in vitro reconstituted chromatin as response to external mechanical stress but also into the operation of molecular motors that themselves generate forces and torques on DNA and chromatin. The main goal of the project is to use nanotechnological tools to understand design principles of biomolecules, biomaterials and biological motors, which in turn shall be used to develop smarter nanotools and functional elements.
Summary
DNA metabolism is governed by a delicate balance between compacting the stored genetic information while simultaneously ensuring a highly dynamically access to it. This interdisciplinary project aims (i) to understand the mechanics and dynamics of chromatin as well as the mechanism of enzymes involved in DNA metabolism on a molecular level and (ii) to develop new nanometric tools based on optical methods and 3D DNA nanostructures that allow addressing new experimental questions. Within the research project novel nanoscopic detection assays based on the combination of magnetic tweezers and optical methods shall be developed, such as ultra-fast torque spectroscopy and combined FRET-force spectroscopy. Our single-molecule assays shall be applied to study the material properties of self-assembled 3D DNA nanostructures, which shall then be used to set up improved high resolution single-molecule assays. These technological improvements will become key to obtain insight into structure and dynamics of in vitro reconstituted chromatin as response to external mechanical stress but also into the operation of molecular motors that themselves generate forces and torques on DNA and chromatin. The main goal of the project is to use nanotechnological tools to understand design principles of biomolecules, biomaterials and biological motors, which in turn shall be used to develop smarter nanotools and functional elements.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-01-01, End date: 2016-10-31
Project acronym EPIGENOME
Project Understanding epigenetic mechanisms of complex genome editing in eukaryotes
Researcher (PI) Mariusz Nowacki
Host Institution (HI) UNIVERSITAET BERN
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
Summary The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate’s genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The ‘genome scanning’ model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a ‘thermodynamic’ problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
Summary
The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate’s genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The ‘genome scanning’ model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a ‘thermodynamic’ problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
