Project acronym AGGLONANOCOAT
Project The interplay between agglomeration and coating of nanoparticles in the gas phase
Researcher (PI) Jan Rudolf Van Ommen
Host Institution (HI) TECHNISCHE UNIVERSITEIT DELFT
Call Details Starting Grant (StG), PE8, ERC-2011-StG_20101014
Summary This proposal aims to develop a generic synthesis approach for core-shell nanoparticles by unravelling the relevant mechanisms. Core-shell nanoparticles have high potential in heterogeneous catalysis, energy storage, and medical applications. However, on a fundamental level there is currently a poor understanding of how to produce such nanostructured particles in a controllable and scalable manner.
The main barriers to achieving this goal are understanding how nanoparticles agglomerate to loose dynamic clusters and controlling the agglomeration process in gas flows during coating, such that uniform coatings can be made. This is very challenging because of the two-way coupling between agglomeration and coating. During the coating we change the particle surfaces and thus the way the particles stick together. Correspondingly, the stickiness of particles determines how easy reactants can reach the surface.
Innovatively the project will be the first systematic study into this multi-scale phenomenon with investigations at all relevant length scales. Current synthesis approaches – mostly carried out in the liquid phase – are typically developed case by case. I will coat nanoparticles in the gas phase with atomic layer deposition (ALD): a technique from the semi-conductor industry that can deposit a wide range of materials. ALD applied to flat substrates offers excellent control over layer thickness. I will investigate the modification of single particle surfaces, particle-particle interaction, the structure of agglomerates, and the flow behaviour of large number of agglomerates. To this end, I will apply a multidisciplinary approach, combining disciplines as physical chemistry, fluid dynamics, and reaction engineering.
Summary
This proposal aims to develop a generic synthesis approach for core-shell nanoparticles by unravelling the relevant mechanisms. Core-shell nanoparticles have high potential in heterogeneous catalysis, energy storage, and medical applications. However, on a fundamental level there is currently a poor understanding of how to produce such nanostructured particles in a controllable and scalable manner.
The main barriers to achieving this goal are understanding how nanoparticles agglomerate to loose dynamic clusters and controlling the agglomeration process in gas flows during coating, such that uniform coatings can be made. This is very challenging because of the two-way coupling between agglomeration and coating. During the coating we change the particle surfaces and thus the way the particles stick together. Correspondingly, the stickiness of particles determines how easy reactants can reach the surface.
Innovatively the project will be the first systematic study into this multi-scale phenomenon with investigations at all relevant length scales. Current synthesis approaches – mostly carried out in the liquid phase – are typically developed case by case. I will coat nanoparticles in the gas phase with atomic layer deposition (ALD): a technique from the semi-conductor industry that can deposit a wide range of materials. ALD applied to flat substrates offers excellent control over layer thickness. I will investigate the modification of single particle surfaces, particle-particle interaction, the structure of agglomerates, and the flow behaviour of large number of agglomerates. To this end, I will apply a multidisciplinary approach, combining disciplines as physical chemistry, fluid dynamics, and reaction engineering.
Max ERC Funding
1 409 952 €
Duration
Start date: 2011-12-01, End date: 2016-11-30
Project acronym CALMIRS
Project RNA-based regulation of signal transduction –
Regulation of calcineurin/NFAT signaling by microRNA-based mechanisms
Researcher (PI) Leon Johannes De Windt
Host Institution (HI) UNIVERSITEIT MAASTRICHT
Call Details Starting Grant (StG), LS4, ERC-2012-StG_20111109
Summary "Heart failure is a serious clinical disorder that represents the primary cause of hospitalization and death in Europe and the United States. There is a dire need for new paradigms and therapeutic approaches for treatment of this devastating disease. The heart responds to mechanical load and various extracellular stimuli by hypertrophic growth and sustained pathological hypertrophy is a major clinical predictor of heart failure. A variety of stress-responsive signaling pathways promote cardiac hypertrophy, but the precise mechanisms that link these pathways to cardiac disease are only beginning to be unveiled. Signal transduction is traditionally concentrated on the protein coding part of the genome, but it is now appreciated that the protein coding part of the genome only constitutes 1.5% of the genome. RNA based mechanisms may provide a more complete understanding of the fundamentals of cellular signaling. As a proof-of-principle, we focus on a principal hypertrophic signaling cascade, cardiac calcineurin/NFAT signaling. Here we will establish that microRNAs are intimately interwoven with this signaling cascade, influence signaling strength by unexpected upstream mechanisms. Secondly, we will firmly establish that microRNA target genes critically contribute to genesis of heart failure. Third, the surprising stability of circulating microRNAs has opened the possibility to develop the next generation of biomarkers and provide unexpected mechanisms how genetic information is transported between cells in multicellular organs and fascilitate inter-cellular communication. Finally, microRNA-based therapeutic silencing is remarkably powerful and offers opportunities to specifically intervene in pathological signaling as the next generation heart failure therapeutics. CALMIRS aims to mine the wealth of these RNA mechanisms to enable the development of next generation RNA based signal transduction biology, with surprising new diagnostic and therapeutic opportunities."
Summary
"Heart failure is a serious clinical disorder that represents the primary cause of hospitalization and death in Europe and the United States. There is a dire need for new paradigms and therapeutic approaches for treatment of this devastating disease. The heart responds to mechanical load and various extracellular stimuli by hypertrophic growth and sustained pathological hypertrophy is a major clinical predictor of heart failure. A variety of stress-responsive signaling pathways promote cardiac hypertrophy, but the precise mechanisms that link these pathways to cardiac disease are only beginning to be unveiled. Signal transduction is traditionally concentrated on the protein coding part of the genome, but it is now appreciated that the protein coding part of the genome only constitutes 1.5% of the genome. RNA based mechanisms may provide a more complete understanding of the fundamentals of cellular signaling. As a proof-of-principle, we focus on a principal hypertrophic signaling cascade, cardiac calcineurin/NFAT signaling. Here we will establish that microRNAs are intimately interwoven with this signaling cascade, influence signaling strength by unexpected upstream mechanisms. Secondly, we will firmly establish that microRNA target genes critically contribute to genesis of heart failure. Third, the surprising stability of circulating microRNAs has opened the possibility to develop the next generation of biomarkers and provide unexpected mechanisms how genetic information is transported between cells in multicellular organs and fascilitate inter-cellular communication. Finally, microRNA-based therapeutic silencing is remarkably powerful and offers opportunities to specifically intervene in pathological signaling as the next generation heart failure therapeutics. CALMIRS aims to mine the wealth of these RNA mechanisms to enable the development of next generation RNA based signal transduction biology, with surprising new diagnostic and therapeutic opportunities."
Max ERC Funding
1 499 528 €
Duration
Start date: 2013-02-01, End date: 2018-01-31
Project acronym CD-LINK
Project Celiac disease: from lincRNAs to disease mechanism
Researcher (PI) Tjitske Nienke Wijmenga
Host Institution (HI) ACADEMISCH ZIEKENHUIS GRONINGEN
Call Details Advanced Grant (AdG), LS2, ERC-2012-ADG_20120314
Summary Celiac disease affects at least 1% of the world population. Its onset is triggered by gluten, a common dietary protein, however, its etiology is poorly understood. More than 80% of patients are not properly diagnosed and they therefore do not follow a gluten-free diet, thereby increasing their risk for disease-associated complications and early death. A better understanding of the disease biology would improve the diagnosis, prevention, and treatment of celiac disease.
This project investigates the disease mechanisms in celiac disease by using predisposing genes and genetic variants as disease initiating factors. Specifically, it will investigate if long, intergenic non-coding RNAs (lincRNAs) are causally involved in celiac disease pathogenesis by regulating protein-coding genes and pathways associated with the disease.
This project is based on two important observations by my group: (1) Our genetic studies, which led to identifying 39 celiac disease risk loci, suggest that the mechanism underlying the disease is largely governed by dysregulation of gene expression. (2) We uncovered a previously unrecognized role for lincRNAs that provides clues as to exactly how genetic variation causes disease, as this class of biologically important RNA molecules regulate gene expression.
The research will be performed in CD4+ T cells, a severely affected cell type in disease pathology. I will first use celiac disease-associated protein-coding genes to delineate their regulatory pathways and then study the transcriptional programs of lincRNAs present in celiac disease loci. Next I will combine the information and investigate if the expressed lincRNAs modulate the pathways and affect T cell function, thereby discovering if lincRNAs are a missing link between non-coding genetic variation and protein-coding genes. Our findings may well lead to potential therapeutic targets and provide a solid scientific basis for new diagnostic markers, particularly biomarkers, based on genetics.
Summary
Celiac disease affects at least 1% of the world population. Its onset is triggered by gluten, a common dietary protein, however, its etiology is poorly understood. More than 80% of patients are not properly diagnosed and they therefore do not follow a gluten-free diet, thereby increasing their risk for disease-associated complications and early death. A better understanding of the disease biology would improve the diagnosis, prevention, and treatment of celiac disease.
This project investigates the disease mechanisms in celiac disease by using predisposing genes and genetic variants as disease initiating factors. Specifically, it will investigate if long, intergenic non-coding RNAs (lincRNAs) are causally involved in celiac disease pathogenesis by regulating protein-coding genes and pathways associated with the disease.
This project is based on two important observations by my group: (1) Our genetic studies, which led to identifying 39 celiac disease risk loci, suggest that the mechanism underlying the disease is largely governed by dysregulation of gene expression. (2) We uncovered a previously unrecognized role for lincRNAs that provides clues as to exactly how genetic variation causes disease, as this class of biologically important RNA molecules regulate gene expression.
The research will be performed in CD4+ T cells, a severely affected cell type in disease pathology. I will first use celiac disease-associated protein-coding genes to delineate their regulatory pathways and then study the transcriptional programs of lincRNAs present in celiac disease loci. Next I will combine the information and investigate if the expressed lincRNAs modulate the pathways and affect T cell function, thereby discovering if lincRNAs are a missing link between non-coding genetic variation and protein-coding genes. Our findings may well lead to potential therapeutic targets and provide a solid scientific basis for new diagnostic markers, particularly biomarkers, based on genetics.
Max ERC Funding
2 319 914 €
Duration
Start date: 2013-02-01, End date: 2018-11-30
Project acronym CHROMATINPRINCIPLES
Project Principles of Chromatin Organization
Researcher (PI) Bas Van Steensel
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary Chromatin is the ensemble of genomic DNA and hundreds of structural and regulatory proteins. Together these proteins govern the gene expression program of a cell. While biochemical and genetic approaches have tought us much about interactions between individual chromatin proteins, we still lack a “big picture” of chromatin: how is the entire interaction network of chromatin proteins organized?
My lab discovered that chromatin in Drosophila consists of a limited number of principal types that partition the genome into domains with distinct regulatory properties. Among these is BLACK chromatin, a novel repressive type of chromatin that covers nearly half of the fly genome. It is still largely unclear how these different chromatin types are formed, how they are targeted to specific genomic regions, and how they interact with each other.
Here, I propose a combination of systematic approaches aimed to gain insight into the basic mechanisms that drive the partioning of the genome into distinct chromatin types. New genomics techniques, developed in my laboratory, will be used to construct an integrated view of the interplay of more than one hundred representative chromatin proteins with each other and with sequence elements in the genome. Specifically, we will: (1) Study the genome-wide dynamic repositioning of chromatin domains during development in relation to gene regulation; (2) Use a novel and versatile parallel genome-wide reporter assay to dissect the interplay among DNA sequences and chromatin types; (3) Combine computational modeling with a high-throughput genome-wide assay to uncover the network of interactions responsible for the formation of the principal chromatin types; (4) Dissect the molecular architecture of BLACK chromatin and its role in gene repression.
The results will provide understanding of the basic principles that govern the structure and composition of chromatin, and reveal how the principal chromatin types together direct gene expression.
Summary
Chromatin is the ensemble of genomic DNA and hundreds of structural and regulatory proteins. Together these proteins govern the gene expression program of a cell. While biochemical and genetic approaches have tought us much about interactions between individual chromatin proteins, we still lack a “big picture” of chromatin: how is the entire interaction network of chromatin proteins organized?
My lab discovered that chromatin in Drosophila consists of a limited number of principal types that partition the genome into domains with distinct regulatory properties. Among these is BLACK chromatin, a novel repressive type of chromatin that covers nearly half of the fly genome. It is still largely unclear how these different chromatin types are formed, how they are targeted to specific genomic regions, and how they interact with each other.
Here, I propose a combination of systematic approaches aimed to gain insight into the basic mechanisms that drive the partioning of the genome into distinct chromatin types. New genomics techniques, developed in my laboratory, will be used to construct an integrated view of the interplay of more than one hundred representative chromatin proteins with each other and with sequence elements in the genome. Specifically, we will: (1) Study the genome-wide dynamic repositioning of chromatin domains during development in relation to gene regulation; (2) Use a novel and versatile parallel genome-wide reporter assay to dissect the interplay among DNA sequences and chromatin types; (3) Combine computational modeling with a high-throughput genome-wide assay to uncover the network of interactions responsible for the formation of the principal chromatin types; (4) Dissect the molecular architecture of BLACK chromatin and its role in gene repression.
The results will provide understanding of the basic principles that govern the structure and composition of chromatin, and reveal how the principal chromatin types together direct gene expression.
Max ERC Funding
2 495 080 €
Duration
Start date: 2012-03-01, End date: 2017-02-28
Project acronym DENOVO
Project Detection and interpretation of de novo mutations and structural genomic variations in mental retardation
Researcher (PI) Joris Andre Veltman
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Mental retardation, like most common neurodevelopmental and psychiatric diseases, shows a strong genetic component, but these underlying genetic causes remain largely unknown. For a long time it was hypothesized that these kind of common diseases are mainly caused by common inherited genetic variants with reduced penetrance. In contrast to this common variant-common disease hypothesis, I here hypothesize that a large proportion of this so-called “missing heritability” for conditions such as mental retardation, schizophrenia, and autism lies in de novo genetic variation that is rapidly eliminated from the population because individuals with such diseases have severely compromised fecundity.
My previous work using microarrays has already demonstrated de novo genomic copy number variations in mental retardation and in schizophrenia. However, microarrays do not allow us to capture the most common form of de novo mutations, those occurring at the nucleotide level. Technological innovations now for the first time allow us to comprehensively study the entire genome of an individual for genomic variations at all levels. In this project I will explore the de novo mutation hypothesis in whole exome and whole genome sequence data from patients with mental retardation. I will optimize and apply whole genome sequencing strategies using patient-parent trios, both in rare mental retardation syndromes as well as common forms of mental retardation. Guidelines for pathogenicity will be established by computational studies aimed at unraveling genotype-phenotype correlations in these family-based genome sequence type datasets.
This project will contribute significantly to resolving the genetic causes of reproductively lethal disorders such as mental retardation, provide critical knowledge on the frequency and consequences of de novo mutations in our genome and help to establish medical genome sequencing as a routine diagnostic approach.
Summary
Mental retardation, like most common neurodevelopmental and psychiatric diseases, shows a strong genetic component, but these underlying genetic causes remain largely unknown. For a long time it was hypothesized that these kind of common diseases are mainly caused by common inherited genetic variants with reduced penetrance. In contrast to this common variant-common disease hypothesis, I here hypothesize that a large proportion of this so-called “missing heritability” for conditions such as mental retardation, schizophrenia, and autism lies in de novo genetic variation that is rapidly eliminated from the population because individuals with such diseases have severely compromised fecundity.
My previous work using microarrays has already demonstrated de novo genomic copy number variations in mental retardation and in schizophrenia. However, microarrays do not allow us to capture the most common form of de novo mutations, those occurring at the nucleotide level. Technological innovations now for the first time allow us to comprehensively study the entire genome of an individual for genomic variations at all levels. In this project I will explore the de novo mutation hypothesis in whole exome and whole genome sequence data from patients with mental retardation. I will optimize and apply whole genome sequencing strategies using patient-parent trios, both in rare mental retardation syndromes as well as common forms of mental retardation. Guidelines for pathogenicity will be established by computational studies aimed at unraveling genotype-phenotype correlations in these family-based genome sequence type datasets.
This project will contribute significantly to resolving the genetic causes of reproductively lethal disorders such as mental retardation, provide critical knowledge on the frequency and consequences of de novo mutations in our genome and help to establish medical genome sequencing as a routine diagnostic approach.
Max ERC Funding
1 499 154 €
Duration
Start date: 2012-02-01, End date: 2017-01-31
Project acronym enhReg
Project Exploring enhancers’ Achilles Heel
Researcher (PI) Reuven Agami
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Advanced Grant (AdG), LS2, ERC-2012-ADG_20120314
Summary Enhancers are genomic domains that regulate transcription of distantly located genes and that are characterized by specific chromatin signatures of histone methylation and acetylation patterns. Interestingly, RNA polymerase II (RNAPII) binds to a subset of enhancers and produces transcripts, called enhancer RNAs (eRNAs). These are produced bi-directionally and, in contrast to mRNAs and many other non-coding RNAs, are not polyadenylated. Generally, the transcription of eRNAs was shown to positively correlate with mRNA levels of surrounding protein-coding genes. However, it is unclear if eRNAs carry a transcriptional function.
p53 is a transcription factor and tumor suppressor that is very frequently mutated in cancer. Chromatin-binding profiles reveal specific interactions of p53 with promoter regions of nearby genes, within genes, but also with remote regions located more than 50 kbps away from any known gene. Interestingly, many of these remote regions possess evolutionary highly conserved p53-binding sites and all known hallmarks of enhancer regions, as well as binding of RNAPII. We found out that many remote p53-bound domains are indeed p53-dependent eRNA-producing enhancers, and, most importantly, eRNA production was required for transcriptional induction of distal genes and for p53-dependent cellular control.
Here we will:
1. Investigate in detail the mechanism of action and function of p53-dependent eRNAs.
2. Expand studies to identify eRNAs with oncogenic function.
3. Develop efficient ways to target eRNAs.
4. Target eRNAs and study their capacity to inhibit tumorigenicity.
As eRNAs are mediators of enhancer activity with sequence specific content and sensitivity to siRNA targeting, they might be the Achilles heel through which oncogenic enhancer activity could be suppressed. Our study will elucidate a novel layer of gene regulation and holds promise for opening up new opportunities to affect cancer-related cellular programs in very specific and effectiv
Summary
Enhancers are genomic domains that regulate transcription of distantly located genes and that are characterized by specific chromatin signatures of histone methylation and acetylation patterns. Interestingly, RNA polymerase II (RNAPII) binds to a subset of enhancers and produces transcripts, called enhancer RNAs (eRNAs). These are produced bi-directionally and, in contrast to mRNAs and many other non-coding RNAs, are not polyadenylated. Generally, the transcription of eRNAs was shown to positively correlate with mRNA levels of surrounding protein-coding genes. However, it is unclear if eRNAs carry a transcriptional function.
p53 is a transcription factor and tumor suppressor that is very frequently mutated in cancer. Chromatin-binding profiles reveal specific interactions of p53 with promoter regions of nearby genes, within genes, but also with remote regions located more than 50 kbps away from any known gene. Interestingly, many of these remote regions possess evolutionary highly conserved p53-binding sites and all known hallmarks of enhancer regions, as well as binding of RNAPII. We found out that many remote p53-bound domains are indeed p53-dependent eRNA-producing enhancers, and, most importantly, eRNA production was required for transcriptional induction of distal genes and for p53-dependent cellular control.
Here we will:
1. Investigate in detail the mechanism of action and function of p53-dependent eRNAs.
2. Expand studies to identify eRNAs with oncogenic function.
3. Develop efficient ways to target eRNAs.
4. Target eRNAs and study their capacity to inhibit tumorigenicity.
As eRNAs are mediators of enhancer activity with sequence specific content and sensitivity to siRNA targeting, they might be the Achilles heel through which oncogenic enhancer activity could be suppressed. Our study will elucidate a novel layer of gene regulation and holds promise for opening up new opportunities to affect cancer-related cellular programs in very specific and effectiv
Max ERC Funding
2 176 840 €
Duration
Start date: 2013-10-01, End date: 2018-09-30
Project acronym EVOSYSBIO
Project Systems biology meets evolutionary theory: modeling the genetics and adaptation of complex traits
Researcher (PI) Gerrit Sander Van Doorn
Host Institution (HI) RIJKSUNIVERSITEIT GRONINGEN
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary "As we learn more about the mechanisms of development, it remains a challenge to understand the relationship between molecular processes and functional characteristics of the organism. The complexity of the networks that link genes and phenotypes is nearly ignored by evolutionary theory, which builds on simple phenomenological models of the genotype-phenotype relationship. These models treat development as a black box, leaving mainstream evolutionary theory ill-equipped to explain how molecular mechanisms evolve. In order to resolve this problem, the current proposal develops a framework for understanding the evolution of complex traits and their genetic basis, integrating methods from systems biology and evolutionary genetics. This novel strategy is first applied to bacterial chemotaxis, a prototype for studying the molecular basis of emergent behavior and its response to selection. A second project examines evolutionary diversification by modeling the origin of distinct ecotypes observed in evolution experiments with Escherichia coli. In both cases, I employ systems-biology models to reconstruct the relationship between molecular mechanisms and phenotypic characters under selection and then apply population-genetic techniques to study how populations evolve on these landscapes. The work on microbial model systems is complemented by conceptual analyses that examine how sexual populations evolve on complex adaptive landscapes. I will study whether higher organisms differ from bacteria in the way they realize evolutionary innovations and whether the high rate of recombination in sexual species has an effect on the structure of molecular interactions. This research will also clarify what signatures of selection are likely to be found in molecular networks. A final research aim is to delineate under what conditions phenotypic evolution can be studied without knowledge of molecular details, which is still the common situation in evolutionary biology."
Summary
"As we learn more about the mechanisms of development, it remains a challenge to understand the relationship between molecular processes and functional characteristics of the organism. The complexity of the networks that link genes and phenotypes is nearly ignored by evolutionary theory, which builds on simple phenomenological models of the genotype-phenotype relationship. These models treat development as a black box, leaving mainstream evolutionary theory ill-equipped to explain how molecular mechanisms evolve. In order to resolve this problem, the current proposal develops a framework for understanding the evolution of complex traits and their genetic basis, integrating methods from systems biology and evolutionary genetics. This novel strategy is first applied to bacterial chemotaxis, a prototype for studying the molecular basis of emergent behavior and its response to selection. A second project examines evolutionary diversification by modeling the origin of distinct ecotypes observed in evolution experiments with Escherichia coli. In both cases, I employ systems-biology models to reconstruct the relationship between molecular mechanisms and phenotypic characters under selection and then apply population-genetic techniques to study how populations evolve on these landscapes. The work on microbial model systems is complemented by conceptual analyses that examine how sexual populations evolve on complex adaptive landscapes. I will study whether higher organisms differ from bacteria in the way they realize evolutionary innovations and whether the high rate of recombination in sexual species has an effect on the structure of molecular interactions. This research will also clarify what signatures of selection are likely to be found in molecular networks. A final research aim is to delineate under what conditions phenotypic evolution can be studied without knowledge of molecular details, which is still the common situation in evolutionary biology."
Max ERC Funding
1 452 478 €
Duration
Start date: 2012-09-01, End date: 2017-08-31
Project acronym GENENOISECONTROL
Project Controlling stochastic gene expression during development and stem cell differentiation
Researcher (PI) Alexander Van Oudenaarden
Host Institution (HI) KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Call Details Advanced Grant (AdG), LS2, ERC-2011-ADG_20110310
Summary The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogenous environments vary, suggesting that randomness in developmental processes such as gene expression may also generate diversity. My laboratory has intensively studied stochastic gene expression in microbial systems and more recently started to apply these concepts to multicellular organisms and stem cells. One of the major lessons learned from our work and others is that microbial systems tend to exploit stochastic gene expression by introducing phenotypic diversity into the population. However it is an open question whether stochastic gene expression benefits or hinders decision-making by cells in a developing embryo. On the one hand, the gene expression patterns of different cells during metazoan development must be aligned either to ensure proper tissue formation or maintain a coordinated timing of developmental events. This suggests that stochastic fluctuations in gene expression may be controlled or their effects may be buffered under normal conditions. On the other hand, stem cells might use fluctuations to prime differentiation. A stem cell might continuously fluctuate between different primed states each biased towards a different germ layer fate. As soon as an external differentiation signal appears the cell would rapidly differentiate towards the fate that was stochastically selected. The overarching goal of this proposal is to the understand how stochastic gene expression is controlled, or utilized, during development and stem cell differentiation using the nematode worm Caenorhabditis elegans and murine embryonic stem cells as experimental model systems. To obtain this goal we will use a combination of quantitative experiments, theoretical and computational approaches, and the development of novel technology.
Summary
The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogenous environments vary, suggesting that randomness in developmental processes such as gene expression may also generate diversity. My laboratory has intensively studied stochastic gene expression in microbial systems and more recently started to apply these concepts to multicellular organisms and stem cells. One of the major lessons learned from our work and others is that microbial systems tend to exploit stochastic gene expression by introducing phenotypic diversity into the population. However it is an open question whether stochastic gene expression benefits or hinders decision-making by cells in a developing embryo. On the one hand, the gene expression patterns of different cells during metazoan development must be aligned either to ensure proper tissue formation or maintain a coordinated timing of developmental events. This suggests that stochastic fluctuations in gene expression may be controlled or their effects may be buffered under normal conditions. On the other hand, stem cells might use fluctuations to prime differentiation. A stem cell might continuously fluctuate between different primed states each biased towards a different germ layer fate. As soon as an external differentiation signal appears the cell would rapidly differentiate towards the fate that was stochastically selected. The overarching goal of this proposal is to the understand how stochastic gene expression is controlled, or utilized, during development and stem cell differentiation using the nematode worm Caenorhabditis elegans and murine embryonic stem cells as experimental model systems. To obtain this goal we will use a combination of quantitative experiments, theoretical and computational approaches, and the development of novel technology.
Max ERC Funding
2 500 000 €
Duration
Start date: 2012-04-01, End date: 2017-03-31
Project acronym HEAVYMETHYL
Project Regulation of gene expression and cell fate by DNA (hydroxy)methylation
Researcher (PI) Michiel Vermeulen
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary (Hydroxy)methylation of cytosine residues in eukaryotic DNA represents a major means to regulate gene expression during development. These modifications are considered to be epigenetic marks, since they have a profound impact on phenotype, but are inherited from mother to daughter cells independent of the underlying DNA sequence. Large efforts are currently underway to profile genome-wide DNA (hydroxy)methylation patterns in model organisms and in clinical studies, since aberrant DNA (hydroxy)methylation is a hallmark of cancer. Strikingly, the molecular mechanisms underlying the link between DNA (hydroxy)methylation and gene expression remain elusive. Although causal links are thought to arise from differential recruitment of transcription factors to (hydroxy)methylated DNA in a regulated manner during development, technical limitations have thus far prevented unbiased interaction screenings to investigate this hypothesis in detail. By using a unique combination of state-of-the-art quantitative mass spectrometry-based proteomics technology, genomics approaches and biochemical experiments, I will systematically investigate which proteins interact with or are repelled by (hydroxy)methylated DNA during stem cell differentiation into a neuronal lineage. Furthermore, I will investigate whether and to what extent these interactions regulate gene expression programs and lineage commitment. The results of these studies will reveal the mechanisms through which dynamic DNA (hydroxy)methylation patterns dictate cellular responses. This is anticipated to significantly increase our understanding of eukaryotic development and the role of epigenetics herein. Furthermore, these studies will pave the way for designing strategies aimed at interfering with altered epigenetics patterns in disease.
Summary
(Hydroxy)methylation of cytosine residues in eukaryotic DNA represents a major means to regulate gene expression during development. These modifications are considered to be epigenetic marks, since they have a profound impact on phenotype, but are inherited from mother to daughter cells independent of the underlying DNA sequence. Large efforts are currently underway to profile genome-wide DNA (hydroxy)methylation patterns in model organisms and in clinical studies, since aberrant DNA (hydroxy)methylation is a hallmark of cancer. Strikingly, the molecular mechanisms underlying the link between DNA (hydroxy)methylation and gene expression remain elusive. Although causal links are thought to arise from differential recruitment of transcription factors to (hydroxy)methylated DNA in a regulated manner during development, technical limitations have thus far prevented unbiased interaction screenings to investigate this hypothesis in detail. By using a unique combination of state-of-the-art quantitative mass spectrometry-based proteomics technology, genomics approaches and biochemical experiments, I will systematically investigate which proteins interact with or are repelled by (hydroxy)methylated DNA during stem cell differentiation into a neuronal lineage. Furthermore, I will investigate whether and to what extent these interactions regulate gene expression programs and lineage commitment. The results of these studies will reveal the mechanisms through which dynamic DNA (hydroxy)methylation patterns dictate cellular responses. This is anticipated to significantly increase our understanding of eukaryotic development and the role of epigenetics herein. Furthermore, these studies will pave the way for designing strategies aimed at interfering with altered epigenetics patterns in disease.
Max ERC Funding
1 499 776 €
Duration
Start date: 2013-10-01, End date: 2018-09-30
Project acronym MacModel
Project Harvesting the power of a new model organism: stem cells, regeneration and ageing in Macrostomum lignano
Researcher (PI) Eugene Berezikov
Host Institution (HI) ACADEMISCH ZIEKENHUIS GRONINGEN
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary The ‘stem-cell theory’ of ageing posits that the functional decline in adult stem cells is one of the factors contributing to ageing. Importantly, the number of stem cells does not diminish with age in many tissues but rather there are intrinsic and extrinsic changes that affect their functionality. Is it possible to reverse these changes? Experiments in the emerging model Macrostomum lignano suggest that this is indeed the case. Remarkably, induced regeneration in this animal leads to extended lifespan: repeated amputation, followed by regeneration, results in animals that live far beyond the median lifespan of 205 days. Regeneration in M. lignano is facilitated by stem cells called neoblasts, and it appears that regeneration resets the ‘ageing program’ in these animals.
Due to its high regeneration capacity, small size, transparency and clear morphology, ease of culture, short generation time and amenability to genetic manipulation, M. lignano has great potential as a model organism for stem cell research. I have recently started developing genomic and genetic tools and resources for this model, and at present my group has generated a draft genome assembly, produced de novo transcriptome assembly, discovered several neoblast marker genes and made the first stable transgenic lines in this animal.
Here I propose to study molecular mechanisms underlying rejuvenation in M. lignano, and to further advance M. lignano as a model organism through development of missing genetic tools and resources. I will address how young, aged and regenerated worms differ in their gene and small RNA expression profiles, and what are the differences and variation levels between neoblasts of young, old and regenerated animals. The biological roles of the identified candidate genes and their effects on the lifespan and neoblast activity will be investigated. In parallel, methods for efficient transgenesis and gene manipulation will be developed, and the genome annotation improved.
Summary
The ‘stem-cell theory’ of ageing posits that the functional decline in adult stem cells is one of the factors contributing to ageing. Importantly, the number of stem cells does not diminish with age in many tissues but rather there are intrinsic and extrinsic changes that affect their functionality. Is it possible to reverse these changes? Experiments in the emerging model Macrostomum lignano suggest that this is indeed the case. Remarkably, induced regeneration in this animal leads to extended lifespan: repeated amputation, followed by regeneration, results in animals that live far beyond the median lifespan of 205 days. Regeneration in M. lignano is facilitated by stem cells called neoblasts, and it appears that regeneration resets the ‘ageing program’ in these animals.
Due to its high regeneration capacity, small size, transparency and clear morphology, ease of culture, short generation time and amenability to genetic manipulation, M. lignano has great potential as a model organism for stem cell research. I have recently started developing genomic and genetic tools and resources for this model, and at present my group has generated a draft genome assembly, produced de novo transcriptome assembly, discovered several neoblast marker genes and made the first stable transgenic lines in this animal.
Here I propose to study molecular mechanisms underlying rejuvenation in M. lignano, and to further advance M. lignano as a model organism through development of missing genetic tools and resources. I will address how young, aged and regenerated worms differ in their gene and small RNA expression profiles, and what are the differences and variation levels between neoblasts of young, old and regenerated animals. The biological roles of the identified candidate genes and their effects on the lifespan and neoblast activity will be investigated. In parallel, methods for efficient transgenesis and gene manipulation will be developed, and the genome annotation improved.
Max ERC Funding
1 499 723 €
Duration
Start date: 2012-11-01, End date: 2017-10-31
