Project acronym Dam2Age
Project DNA Damage and Repair and its Impact on Healthy Ageing
Researcher (PI) Jan HOEIJMAKERS
Host Institution (HI) ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Call Details Advanced Grant (AdG), LS1, ERC-2016-ADG
Summary We pioneered an initially highly controversial connection between DNA damage and (accelerated) aging. In the previous ERC grant ‘DamAge’ we reached the stage that (segmental) aging in DNA repair-deficient mice can be largely controlled. The severity of the repair defect determines the rate of segmental aging; the repair pathways affected influence which organs age fast; conditional repair mutants allow targeting accelerated aging to any organ. Importantly, we found that dietary restriction (DR), the only universal intervention known to delay aging, extends remaining life- and healthspan in progeroid Ercc1Δ/- mutants by 200% (see Vermeij et al., Nature 2016 and fig.2). Also Xpg-/- progeroid repair mice strongly benefit from DR, generalizing this finding. The prominent Alzheimer- and Parkinson-like neurodegeneration is even retarded up to 30-fold(!) disclosing powerful untapped reserves unleashed by 30% less food, with enormous clinical potential. Also we discovered that in accelerated and normal aging gene expression declines due to accumulating stochastic transcription-blocking lesions and that DR counteracts genomic dysfunction. In Dam2Age we will focus on the cross-talk between DNA damage, aging and DR with emphasis on the relevance for normal aging, elucidate underlying mechanisms and use our unique -for DR research superior- mouse models and a variety of novel assays to search for effective nutritional-pharmacological DR mimetics. This serves as a stepping stone towards potent universal therapy for a range of repair-deficient progeroid syndromes and prevention of many aging-related diseases, most urgently dementia’s, to promote sustained health.
Summary
We pioneered an initially highly controversial connection between DNA damage and (accelerated) aging. In the previous ERC grant ‘DamAge’ we reached the stage that (segmental) aging in DNA repair-deficient mice can be largely controlled. The severity of the repair defect determines the rate of segmental aging; the repair pathways affected influence which organs age fast; conditional repair mutants allow targeting accelerated aging to any organ. Importantly, we found that dietary restriction (DR), the only universal intervention known to delay aging, extends remaining life- and healthspan in progeroid Ercc1Δ/- mutants by 200% (see Vermeij et al., Nature 2016 and fig.2). Also Xpg-/- progeroid repair mice strongly benefit from DR, generalizing this finding. The prominent Alzheimer- and Parkinson-like neurodegeneration is even retarded up to 30-fold(!) disclosing powerful untapped reserves unleashed by 30% less food, with enormous clinical potential. Also we discovered that in accelerated and normal aging gene expression declines due to accumulating stochastic transcription-blocking lesions and that DR counteracts genomic dysfunction. In Dam2Age we will focus on the cross-talk between DNA damage, aging and DR with emphasis on the relevance for normal aging, elucidate underlying mechanisms and use our unique -for DR research superior- mouse models and a variety of novel assays to search for effective nutritional-pharmacological DR mimetics. This serves as a stepping stone towards potent universal therapy for a range of repair-deficient progeroid syndromes and prevention of many aging-related diseases, most urgently dementia’s, to promote sustained health.
Max ERC Funding
2 251 719 €
Duration
Start date: 2017-09-01, End date: 2022-08-31
Project acronym DAMAGE
Project DNA damage and the connection with cancer, premature aging and longevity
Researcher (PI) Jan Hendrik Jozef Hoeijmakers
Host Institution (HI) ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Call Details Advanced Grant (AdG), LS1, ERC-2008-AdG
Summary We study DNA damage and genome stability and its impact on human health using nucleotide excision repair (NER) as paradigm. Patients with NER defects present a perplexing clinical heterogeneity ranging from extreme cancer predisposition to dramatic neurodevelopmental deficits. To elucidate the underlying mechanism we adopted an integral strategy from gene to patient and contributed to resolving the NER reaction in vitro and its dynamic organization in vivo, using molecular genetics, advanced life cell imaging and photobleaching. Mouse NER mutants revealed an unexpected link between DNA damage and (premature) aging, as strong as the DNA damage-cancer connection. We found a striking correlation between type/severity of the repair defect and degree of premature aging, with some mutants dying of aging in 3 weeks! Pathological and functional analysis and expression profiling confirmed that this is bona fide aging. Conditional mutants allowed targeting accelerated aging to specific organs/stages of development e.g. dramatic aging only in brain. Expression profiling revealed that short-lived repair mutants mount a survival response that attempts to extend lifespan by investing in defenses at the expense of growth. The ambitious objective of this multi-disciplinary proposal is to obtain an integral understanding of the biological/medical impact of DNA damage and the important survival response, with emphasis on rational-based prevention and intervention strategies for cancer and other aging-related diseases using the rapidly aging mouse mutants as tools. Triggering the survival response at adulthood is expected to postpone many aging-related diseases including cancer and to strongly improve quality of life at later age. We already identified compounds that influence rapid aging in mice and demonstrated the potency of the survival response to withstand ischemia reperfusion damage. Thus, this proposal addresses the major medical challenges faced by our society.
Summary
We study DNA damage and genome stability and its impact on human health using nucleotide excision repair (NER) as paradigm. Patients with NER defects present a perplexing clinical heterogeneity ranging from extreme cancer predisposition to dramatic neurodevelopmental deficits. To elucidate the underlying mechanism we adopted an integral strategy from gene to patient and contributed to resolving the NER reaction in vitro and its dynamic organization in vivo, using molecular genetics, advanced life cell imaging and photobleaching. Mouse NER mutants revealed an unexpected link between DNA damage and (premature) aging, as strong as the DNA damage-cancer connection. We found a striking correlation between type/severity of the repair defect and degree of premature aging, with some mutants dying of aging in 3 weeks! Pathological and functional analysis and expression profiling confirmed that this is bona fide aging. Conditional mutants allowed targeting accelerated aging to specific organs/stages of development e.g. dramatic aging only in brain. Expression profiling revealed that short-lived repair mutants mount a survival response that attempts to extend lifespan by investing in defenses at the expense of growth. The ambitious objective of this multi-disciplinary proposal is to obtain an integral understanding of the biological/medical impact of DNA damage and the important survival response, with emphasis on rational-based prevention and intervention strategies for cancer and other aging-related diseases using the rapidly aging mouse mutants as tools. Triggering the survival response at adulthood is expected to postpone many aging-related diseases including cancer and to strongly improve quality of life at later age. We already identified compounds that influence rapid aging in mice and demonstrated the potency of the survival response to withstand ischemia reperfusion damage. Thus, this proposal addresses the major medical challenges faced by our society.
Max ERC Funding
2 000 000 €
Duration
Start date: 2010-01-01, End date: 2014-12-31
Project acronym DAMAGE BYPASS
Project Mechanistic analysis of DNA damage bypass in the context of chromatin and genome replication
Researcher (PI) Helle Doerte Ulrich
Host Institution (HI) INSTITUT FUR MOLEKULARE BIOLOGIE GGMBH
Call Details Advanced Grant (AdG), LS1, ERC-2012-ADG_20120314
Summary During its duplication, DNA, the carrier of our genetic information, is particularly vulnerable to decay, and the capacity of cells to deal with replication stress has been recognised as a major factor protecting us from genome instability and cancer. A major pathway that allows cells to overcome or bypass DNA lesions during replication is activated by posttranslational modifications of the sliding clamp protein PCNA. Whereas monoubiquitylation of PCNA allows mutagenic translesion synthesis by damage-tolerant DNA polymerases, polyubiquitylation is required for an error-free pathway that involves template switching to the undamaged sister chromatid, involving a recombination-like mechanism. Hence, damage bypass contributes to genome maintenance, but can itself be a source of genomic instability. It is therefore not surprising that PRR is a highly regulated process whose activity is limited to the appropriate situations by stringent control mechanisms.
The proposed project aims at understanding DNA damage bypass in its cellular context. Using a combination of new and established technology, we will address the role of chromatin dynamics in the reaction, its spatial and temporal control in relation to genome replication, and its coordination with other PCNA-dependent processes in the cell. To this end, we will establish technology to isolate and analyse the composition of damage bypass tracts, develop and implement novel methods to induce lesions and image damage processing in live cells, and exploit a spectrum of biochemical and biophysical techniques to investigate the role of PCNA as a molecular tool-belt in the coordination of its interaction partners. In combination, these approaches will give important insight into how the replication of damaged DNA is managed with high efficiency and accuracy within the cell.
Summary
During its duplication, DNA, the carrier of our genetic information, is particularly vulnerable to decay, and the capacity of cells to deal with replication stress has been recognised as a major factor protecting us from genome instability and cancer. A major pathway that allows cells to overcome or bypass DNA lesions during replication is activated by posttranslational modifications of the sliding clamp protein PCNA. Whereas monoubiquitylation of PCNA allows mutagenic translesion synthesis by damage-tolerant DNA polymerases, polyubiquitylation is required for an error-free pathway that involves template switching to the undamaged sister chromatid, involving a recombination-like mechanism. Hence, damage bypass contributes to genome maintenance, but can itself be a source of genomic instability. It is therefore not surprising that PRR is a highly regulated process whose activity is limited to the appropriate situations by stringent control mechanisms.
The proposed project aims at understanding DNA damage bypass in its cellular context. Using a combination of new and established technology, we will address the role of chromatin dynamics in the reaction, its spatial and temporal control in relation to genome replication, and its coordination with other PCNA-dependent processes in the cell. To this end, we will establish technology to isolate and analyse the composition of damage bypass tracts, develop and implement novel methods to induce lesions and image damage processing in live cells, and exploit a spectrum of biochemical and biophysical techniques to investigate the role of PCNA as a molecular tool-belt in the coordination of its interaction partners. In combination, these approaches will give important insight into how the replication of damaged DNA is managed with high efficiency and accuracy within the cell.
Max ERC Funding
2 476 388 €
Duration
Start date: 2013-03-01, End date: 2018-02-28
Project acronym DDRegulation
Project Regulation of DNA damage responses at the replication fork
Researcher (PI) Niels Mailand
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Consolidator Grant (CoG), LS1, ERC-2013-CoG
Summary This project aims at delineating the regulatory signaling processes that enable cells to overcome DNA damage during DNA replication, a major challenge to the integrity of the genome as the normal replication machinery is unable to replicate past DNA lesions. This may result in collapse of the replication fork, potentially giving rise to gross genomic alterations. To mitigate this threat, all cells have evolved DNA damage bypass strategies such as translesion DNA synthesis (TLS), involving low fidelity DNA polymerases that can replicate damaged DNA, albeit in an error-prone manner, offering a trade-off between limited mutagenesis and gross chromosomal instability. How DNA damage bypass pathways are regulated and integrated with DNA replication and repair remain poorly resolved questions fundamental to understanding genome stability maintenance and disease onset. Regulatory signaling mediated by the small modifier protein ubiquitin has a prominent role in orchestrating the reorganization of the replication fork necessary for overcoming DNA lesions, but this involvement has not been systematically explored. To remedy these gaps in our knowledge, I propose to implement a series of innovative complementary strategies to isolate and identify the regulatory factors and ubiquitin-dependent processes that promote DNA damage responses at the replication fork, allowing for subsequent in-depth characterization of their roles in protecting genome integrity by targeted functional studies. This project will enable an advanced level of mechanistic insight into key regulatory processes underlying replication-associated DNA damage responses that has not been feasible to achieve with exisiting methodologies, providing a realistic outlook for groundbreaking discoveries that will open up many new avenues for further research into mechanisms and biological functions of regulatory signaling processes in the DNA damage response and beyond.
Summary
This project aims at delineating the regulatory signaling processes that enable cells to overcome DNA damage during DNA replication, a major challenge to the integrity of the genome as the normal replication machinery is unable to replicate past DNA lesions. This may result in collapse of the replication fork, potentially giving rise to gross genomic alterations. To mitigate this threat, all cells have evolved DNA damage bypass strategies such as translesion DNA synthesis (TLS), involving low fidelity DNA polymerases that can replicate damaged DNA, albeit in an error-prone manner, offering a trade-off between limited mutagenesis and gross chromosomal instability. How DNA damage bypass pathways are regulated and integrated with DNA replication and repair remain poorly resolved questions fundamental to understanding genome stability maintenance and disease onset. Regulatory signaling mediated by the small modifier protein ubiquitin has a prominent role in orchestrating the reorganization of the replication fork necessary for overcoming DNA lesions, but this involvement has not been systematically explored. To remedy these gaps in our knowledge, I propose to implement a series of innovative complementary strategies to isolate and identify the regulatory factors and ubiquitin-dependent processes that promote DNA damage responses at the replication fork, allowing for subsequent in-depth characterization of their roles in protecting genome integrity by targeted functional studies. This project will enable an advanced level of mechanistic insight into key regulatory processes underlying replication-associated DNA damage responses that has not been feasible to achieve with exisiting methodologies, providing a realistic outlook for groundbreaking discoveries that will open up many new avenues for further research into mechanisms and biological functions of regulatory signaling processes in the DNA damage response and beyond.
Max ERC Funding
1 996 356 €
Duration
Start date: 2014-07-01, End date: 2019-06-30
Project acronym DDRNA
Project A novel direct role of non coding RNA in DNA damage response activation
Researcher (PI) Fabrizio D'adda Di Fagagna
Host Institution (HI) IFOM FONDAZIONE ISTITUTO FIRC DI ONCOLOGIA MOLECOLARE
Call Details Advanced Grant (AdG), LS1, ERC-2012-ADG_20120314
Summary DNA, if damaged, cannot be replaced. If not replaceable, it must be repaired. The so-called “DNA damage response” (DDR) is a coordinate set of evolutionary conserved events that arrest the cell-cycle (DNA damage checkpoint function) in proliferating cells and attempts DNA repair. Until DNA damage has not been repaired in full, cell proliferation is not resumed in normal cells.
DNA damage is a physiological event. Ageing and cancer are both associated with DNA damage accumulation. In the past, we contribute to better understand the mechanisms and the consequences of DNA damage generation and DDR activation in both settings.
We have recently identified a completely hitherto undiscovered level of control of DDR activation, so far considered a proteinaceous only signaling cascade. We have discovered that short RNA species are detectable at DNA damage sites and are necessary for DDR activation at DNA lesions. These RNA species are generated by an evolutionary-conserved RNA processing machinery. However, they serve purposes never reported before.
We believe that our findings change radically our understanding of DDR modulation in mammals and disclose a fertile unspoilt ground for exciting investigations.
Summary
DNA, if damaged, cannot be replaced. If not replaceable, it must be repaired. The so-called “DNA damage response” (DDR) is a coordinate set of evolutionary conserved events that arrest the cell-cycle (DNA damage checkpoint function) in proliferating cells and attempts DNA repair. Until DNA damage has not been repaired in full, cell proliferation is not resumed in normal cells.
DNA damage is a physiological event. Ageing and cancer are both associated with DNA damage accumulation. In the past, we contribute to better understand the mechanisms and the consequences of DNA damage generation and DDR activation in both settings.
We have recently identified a completely hitherto undiscovered level of control of DDR activation, so far considered a proteinaceous only signaling cascade. We have discovered that short RNA species are detectable at DNA damage sites and are necessary for DDR activation at DNA lesions. These RNA species are generated by an evolutionary-conserved RNA processing machinery. However, they serve purposes never reported before.
We believe that our findings change radically our understanding of DDR modulation in mammals and disclose a fertile unspoilt ground for exciting investigations.
Max ERC Funding
2 329 200 €
Duration
Start date: 2013-06-01, End date: 2018-05-31
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 DEAD2THEEND
Project RNA poly(A) tail: the beginning of the end
Researcher (PI) Elena Conti
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Call Details Advanced Grant (AdG), LS1, ERC-2011-ADG_20110310
Summary "The degradation of mature mRNAs has emerged as a key step in the regulation of eukaryotic gene expression. Modulation of the half-life of mRNAs via their degradation is a powerful and versatile mechanism to swiftly alter the expression of proteins in response to changes in physiological conditions. The decay of mRNAs is performed by a set of macromolecular complexes that act in a sequential and coordinated manner, progressively eroding the ends of the transcript until its degradation is complete. These macromolecular assemblies contain only a few catalytically active subunits and a large number of regulatory components. How and why the activities are regulated within the architecture of the complexes is largely unknown. Also unclear are the mechanisms with which the complexes communicate with each other and/or with the changing composition of the nucleic acid. In this project, we will reconstitute the key protein complexes in mRNA decay from recombinant proteins in vitro. Specifically, we will focus on the evolutionary conserved deadenylation, decapping and exosome-Ski complexes. The reconstituted complexes will be used for structural studies to derive atomic models of the holoenzymes using a combination of X-ray crystallography and cryoelectron microscopy. In parallel to obtaining static views of the individual steps in the pathway, we will establish the assays to study how information from one processing step is passed on to the next in a dynamic manner. We will address the basis for the timing and interrelationship of the conserved enzymatic machineries and the influence of the mRNP composition on their activity. Our final goal is to recapitulate the complex behavior of the mRNA decay pathway in vitro. Our lab has extensive experience in biochemical reconstitution of protein complexes, in vitro biochemical assays and X-ray crystallography. In the next five years, we plan to implement cryoelectron microscopy within the scope of this proposal."
Summary
"The degradation of mature mRNAs has emerged as a key step in the regulation of eukaryotic gene expression. Modulation of the half-life of mRNAs via their degradation is a powerful and versatile mechanism to swiftly alter the expression of proteins in response to changes in physiological conditions. The decay of mRNAs is performed by a set of macromolecular complexes that act in a sequential and coordinated manner, progressively eroding the ends of the transcript until its degradation is complete. These macromolecular assemblies contain only a few catalytically active subunits and a large number of regulatory components. How and why the activities are regulated within the architecture of the complexes is largely unknown. Also unclear are the mechanisms with which the complexes communicate with each other and/or with the changing composition of the nucleic acid. In this project, we will reconstitute the key protein complexes in mRNA decay from recombinant proteins in vitro. Specifically, we will focus on the evolutionary conserved deadenylation, decapping and exosome-Ski complexes. The reconstituted complexes will be used for structural studies to derive atomic models of the holoenzymes using a combination of X-ray crystallography and cryoelectron microscopy. In parallel to obtaining static views of the individual steps in the pathway, we will establish the assays to study how information from one processing step is passed on to the next in a dynamic manner. We will address the basis for the timing and interrelationship of the conserved enzymatic machineries and the influence of the mRNP composition on their activity. Our final goal is to recapitulate the complex behavior of the mRNA decay pathway in vitro. Our lab has extensive experience in biochemical reconstitution of protein complexes, in vitro biochemical assays and X-ray crystallography. In the next five years, we plan to implement cryoelectron microscopy within the scope of this proposal."
Max ERC Funding
2 499 344 €
Duration
Start date: 2012-04-01, End date: 2017-03-31
Project acronym DECODINGSUMO
Project Cracking the SUMO Signalling Code
Researcher (PI) Alfredus Cornelis Otto Vertegaal
Host Institution (HI) ACADEMISCH ZIEKENHUIS LEIDEN
Call Details Starting Grant (StG), LS1, ERC-2012-StG_20111109
Summary "Functional activity of proteins is tightly controlled via reversible post-translational modifications including phosphorylation, acetylation and ubiquitylation. These modifications enable the orchestration of cellular responses to a wide variety of stimuli. Due to these modifications, proteomes are overwhelmingly complex. Progress in the field has been greatly accelerated by the development of novel approaches to study these post-translational modifications at a proteome-wide scale using the sensitivity and robustness of mass spectrometry (MS). This has enabled the identification of thousands of dynamically regulated phosphorylation, acetylation and ubiquitylation sites by MS. The functional significance of these modifications is now being addressed worldwide at an unprecedented scale. In contrast, global understanding of ubiquitin-like signalling networks in a site-specific manner is very challenging.
Over the last few years, my lab has established novel methodology for the purification and identification of endogenous SUMO target proteins and SUMOylation sites of endogenous targets. The first aim of this project is to uncover small ubiquitin-like modifier (SUMO) signalling pathways in a site-specific manner at a proteome-wide level.
The second aim of this project is to reveal how SUMOylation cooperates with ubiquitylation to maintain genome integrity. SUMOylation plays a critical role during the DNA damage response, an important barrier against genome instability linked diseases including cancer and neurodegeneration. Selected target proteins will be studied at the functional and mechanistic level to obtain novel insight in cellular processes that protect against genome instability.
The developed methodology is generic and can be applied to study all ubiquitin-like proteins at a proteome-wide level in a site-specific manner, enabling global understanding of ubiquitin-like signalling networks in health and disease."
Summary
"Functional activity of proteins is tightly controlled via reversible post-translational modifications including phosphorylation, acetylation and ubiquitylation. These modifications enable the orchestration of cellular responses to a wide variety of stimuli. Due to these modifications, proteomes are overwhelmingly complex. Progress in the field has been greatly accelerated by the development of novel approaches to study these post-translational modifications at a proteome-wide scale using the sensitivity and robustness of mass spectrometry (MS). This has enabled the identification of thousands of dynamically regulated phosphorylation, acetylation and ubiquitylation sites by MS. The functional significance of these modifications is now being addressed worldwide at an unprecedented scale. In contrast, global understanding of ubiquitin-like signalling networks in a site-specific manner is very challenging.
Over the last few years, my lab has established novel methodology for the purification and identification of endogenous SUMO target proteins and SUMOylation sites of endogenous targets. The first aim of this project is to uncover small ubiquitin-like modifier (SUMO) signalling pathways in a site-specific manner at a proteome-wide level.
The second aim of this project is to reveal how SUMOylation cooperates with ubiquitylation to maintain genome integrity. SUMOylation plays a critical role during the DNA damage response, an important barrier against genome instability linked diseases including cancer and neurodegeneration. Selected target proteins will be studied at the functional and mechanistic level to obtain novel insight in cellular processes that protect against genome instability.
The developed methodology is generic and can be applied to study all ubiquitin-like proteins at a proteome-wide level in a site-specific manner, enabling global understanding of ubiquitin-like signalling networks in health and disease."
Max ERC Funding
1 517 699 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym DECOR
Project Dynamic assembly and exchange of RNA polymerase II CTD factors
Researcher (PI) Richard Stefl
Host Institution (HI) Masarykova univerzita
Call Details Consolidator Grant (CoG), LS1, ERC-2014-CoG
Summary The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Summary
The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Max ERC Funding
1 844 604 €
Duration
Start date: 2015-08-01, End date: 2020-07-31
Project acronym DEFACT
Project DNA repair factories how cells do biochemistry
Researcher (PI) Michael Lisby
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Starting Grant (StG), LS1, ERC-2009-StG
Summary The integrity of a cell's genome is constantly challenged by DNA lesions such as base modifications and DNA strand breaks. A single double-strand break is lethal if unrepaired and may lead to loss-of-heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss if repaired improperly. Such genetic alterations are the main cause of cancer and other genetic diseases. Homologous recombination is an error-free pathway for repairing DNA lesions such as single- and double-strand breaks, and for the restart of collapsed replication forks. This pathway is catalyzed by giga-Dalton protein complexes consisting of dozens of different proteins. These DNA repair factories are able to catalyze complex, multi-step biochemical processes, which have so far failed reconstitution in vitro. The aim of this project is to establish an understanding of how cells catalyze complex biochemical processes such as homologous recombination in vivo. To reach this goal, we will seek to define the complete set of RNA and protein components of DNA repair factories using a combination of genetic, cell biological and biochemical approaches in the yeast Saccharomyces cerevisiae. Further, we will characterize the molecular architecture of DNA repair factories using fluorescence resonance energy transfer (FRET) and by applying systematic hybrid loss-of-heterozygosity (LOH) to physical interactions among DNA repair proteins. Key findings will be extended to metazoans using the chicken DT40 model system. My aim is to determine the fundamental molecular principles that govern protein factories in living cells. As such, our results are likely to be directly relevant to other protein factories such as DNA replication factories, PML bodies, nuclear pore complexes and transcription clusters.
Summary
The integrity of a cell's genome is constantly challenged by DNA lesions such as base modifications and DNA strand breaks. A single double-strand break is lethal if unrepaired and may lead to loss-of-heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss if repaired improperly. Such genetic alterations are the main cause of cancer and other genetic diseases. Homologous recombination is an error-free pathway for repairing DNA lesions such as single- and double-strand breaks, and for the restart of collapsed replication forks. This pathway is catalyzed by giga-Dalton protein complexes consisting of dozens of different proteins. These DNA repair factories are able to catalyze complex, multi-step biochemical processes, which have so far failed reconstitution in vitro. The aim of this project is to establish an understanding of how cells catalyze complex biochemical processes such as homologous recombination in vivo. To reach this goal, we will seek to define the complete set of RNA and protein components of DNA repair factories using a combination of genetic, cell biological and biochemical approaches in the yeast Saccharomyces cerevisiae. Further, we will characterize the molecular architecture of DNA repair factories using fluorescence resonance energy transfer (FRET) and by applying systematic hybrid loss-of-heterozygosity (LOH) to physical interactions among DNA repair proteins. Key findings will be extended to metazoans using the chicken DT40 model system. My aim is to determine the fundamental molecular principles that govern protein factories in living cells. As such, our results are likely to be directly relevant to other protein factories such as DNA replication factories, PML bodies, nuclear pore complexes and transcription clusters.
Max ERC Funding
1 700 030 €
Duration
Start date: 2009-12-01, End date: 2014-11-30
