Project acronym UMICIS
Project Uncultivated Microbes In Situ - a Computational Biology Approach to Determine Molecular Capabilities and Ecological Roles
Researcher (PI) Christian Von Mering
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Starting Grant (StG), LS2, ERC-2009-StG
Summary Most of nature s biodiversity, and many potentially useful metabolic capabilities, remain hidden among the vast numbers of uncharacterized environmental microbes. Because cultivation is still not possible for most of these microbes, cultivation-independent molecular techniques such as polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), or shotgun DNA sequencing have been used in order to study their function and ecology in their natural habitats. However, none of the above techniques have so far been sufficient for any systematic assignment of molecular functions to distinct microbial lineages. Thus, most of the molecular ecology of natural microbes remains elusive. Here, we propose a computational meta-analysis and synthesis of existing and newly generated molecular sequence data sampled directly from the environment combining DNA sequencing data (metagenomics), and proteome expression data (metaproteomics). This analysis will be coupled to computational modelling of genome content evolution at the community level. We will aim to assess how gene repertoires of microbial communities, and their taxonomic compositions, change across distinct environments, in response to changed conditions, and through time. We plan to address fundamental questions in microbial ecology, including the extent of cooperation among members of the communities, stability of community composition at evolutionary timescales, the importance of lateral gene transfers, the extent of functional adaptation/regulation in situ, and whether gene occurrence and expression patterns are diagnostic of community functions and ecological status.
Summary
Most of nature s biodiversity, and many potentially useful metabolic capabilities, remain hidden among the vast numbers of uncharacterized environmental microbes. Because cultivation is still not possible for most of these microbes, cultivation-independent molecular techniques such as polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), or shotgun DNA sequencing have been used in order to study their function and ecology in their natural habitats. However, none of the above techniques have so far been sufficient for any systematic assignment of molecular functions to distinct microbial lineages. Thus, most of the molecular ecology of natural microbes remains elusive. Here, we propose a computational meta-analysis and synthesis of existing and newly generated molecular sequence data sampled directly from the environment combining DNA sequencing data (metagenomics), and proteome expression data (metaproteomics). This analysis will be coupled to computational modelling of genome content evolution at the community level. We will aim to assess how gene repertoires of microbial communities, and their taxonomic compositions, change across distinct environments, in response to changed conditions, and through time. We plan to address fundamental questions in microbial ecology, including the extent of cooperation among members of the communities, stability of community composition at evolutionary timescales, the importance of lateral gene transfers, the extent of functional adaptation/regulation in situ, and whether gene occurrence and expression patterns are diagnostic of community functions and ecological status.
Max ERC Funding
1 129 800 €
Duration
Start date: 2010-02-01, End date: 2016-01-31
Project acronym UNICODE
Project Evolution and Impact of Heterochromatin on a Young Drosophila Y chromosome
Researcher (PI) Qi Zhou
Host Institution (HI) UNIVERSITAT WIEN
Call Details Starting Grant (StG), LS2, ERC-2015-STG
Summary The transition from euchromatin to heterochromatin is a fundamental process that particularly reshaped the epigenomic landscape of Y chromosome. Its definitive genomic underpinning and broad functional impact are still unclear, as heterochromatin (e.g., that of human Y) is usually too repetitive to study. I have previously demonstrated that, the young Y (‘neo-Y’) chromosome of Drosophila miranda has just initiated such a transition, thus is a powerful model to unveil the evolution, regulation and functional interaction of heterochromatin. I showed that this neo-Y still harbours over 1800 genes, and only 20-50% of the sequences are transposable elements (TE). Over five years, I aim to: 1) precisely resolve the structure and insertion sites of TEs as a pre-requisite for studying heterochromatin, by combining state-of-art sequencing and bioinformatic techniques. 2) I will reveal the de novo heterochromatin formation triggered by TE insertions or the heterochromatin/euchromatin boundary shifts on the neo-Y, by comparing the binding profiles of histone modification hallmarks and insulator proteins of D. miranda to its sibling species D. pseudoobscura, which lacks the neo-Y. Such epigenomic changes have likely driven the exaptation or innovation of small RNA pathways that govern the TE mobility. 3) I will then identify the responsible small RNAs and their encoding loci, which are expected to have newly emerged or differentially expressed in D. miranda relative to D. pseudoobscura. 4) Finally, I will develop CRISPR/Cas9 in D. miranda to manipulate the expression of TEs encoding such small RNAs on the neo-Y, in order to scrutinize how TE/heterochromatin evolution on the Y would impact the chromatin landscape of the entire host genome. The combined aim of this multidisciplinary project is to generate a framework for understanding the basic mechanisms of how heterochromatin evolves; and open a new avenue toward the discovery of Y chromosome function beyond male determination.
Summary
The transition from euchromatin to heterochromatin is a fundamental process that particularly reshaped the epigenomic landscape of Y chromosome. Its definitive genomic underpinning and broad functional impact are still unclear, as heterochromatin (e.g., that of human Y) is usually too repetitive to study. I have previously demonstrated that, the young Y (‘neo-Y’) chromosome of Drosophila miranda has just initiated such a transition, thus is a powerful model to unveil the evolution, regulation and functional interaction of heterochromatin. I showed that this neo-Y still harbours over 1800 genes, and only 20-50% of the sequences are transposable elements (TE). Over five years, I aim to: 1) precisely resolve the structure and insertion sites of TEs as a pre-requisite for studying heterochromatin, by combining state-of-art sequencing and bioinformatic techniques. 2) I will reveal the de novo heterochromatin formation triggered by TE insertions or the heterochromatin/euchromatin boundary shifts on the neo-Y, by comparing the binding profiles of histone modification hallmarks and insulator proteins of D. miranda to its sibling species D. pseudoobscura, which lacks the neo-Y. Such epigenomic changes have likely driven the exaptation or innovation of small RNA pathways that govern the TE mobility. 3) I will then identify the responsible small RNAs and their encoding loci, which are expected to have newly emerged or differentially expressed in D. miranda relative to D. pseudoobscura. 4) Finally, I will develop CRISPR/Cas9 in D. miranda to manipulate the expression of TEs encoding such small RNAs on the neo-Y, in order to scrutinize how TE/heterochromatin evolution on the Y would impact the chromatin landscape of the entire host genome. The combined aim of this multidisciplinary project is to generate a framework for understanding the basic mechanisms of how heterochromatin evolves; and open a new avenue toward the discovery of Y chromosome function beyond male determination.
Max ERC Funding
1 971 846 €
Duration
Start date: 2016-08-01, End date: 2021-07-31
Project acronym UPRmt
Project The Mitochondrial Unfolded Protein Response
Researcher (PI) Johan Henri Louise AUWERX
Host Institution (HI) ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Call Details Advanced Grant (AdG), LS2, ERC-2017-ADG
Summary Mitochondria—organelles specialized in energy harvesting through oxidative phosphorylation (Oxphos)—critically influence metabolism, health and lifespan. Evolved from endosymbiotic proteobacteria, mitochondria retained the vestige of the bacterial genome, the mitochondrial DNA, which encodes 13 subunits of the Oxphos complexes, while the remaining ~80 Oxphos components and the rest of the mitochondrial proteome are encoded on nuclear DNA, translated in the cytoplasm and imported in the mitochondria. The control of the mitochondrial proteome by two genomes exposes these organelles to proteotoxic stress in case of an imbalance between the nuclear- and mitochondrial-encoded proteins. Upon such stress, several mitochondrial protein quality control (mtPQC) pathways, including the mitochondrial unfolded protein response (UPRmt), will sense, transmit and re-establish mitochondrial proteostasis through mitonuclear regulatory circuits. Although a robust UPRmt circuit improves health and lifespan in C. elegans, much less is known about mtPQC in vertebrates. We propose here to characterize UPRmt pathways across 3 species by: (1) mapping mammalian UPRmt genes and networks in vivo after the induction of the UPRmt in a large murine genetic reference population at 3 different times throughout life with 2 different inducers; (2) integrating these UPRmt networks with a wide set of clinical, mitochondrial, and molecular phenotypes collected throughout life to establish links between UPRmt mechanisms and health- and lifespan; (3) mechanistically validating the most important UPRmt pathways, using loss-of-function studies in cells, worms and mice; and (4) clinically translating promising UPRmt hits, using genetic association studies in human cohorts. The insight gained will mechanistically define the UPRmt networks from worms to humans and will provide the next step in translating the benefits of activating the UPRmt—initially observed in invertebrates—into targeted human therapies.
Summary
Mitochondria—organelles specialized in energy harvesting through oxidative phosphorylation (Oxphos)—critically influence metabolism, health and lifespan. Evolved from endosymbiotic proteobacteria, mitochondria retained the vestige of the bacterial genome, the mitochondrial DNA, which encodes 13 subunits of the Oxphos complexes, while the remaining ~80 Oxphos components and the rest of the mitochondrial proteome are encoded on nuclear DNA, translated in the cytoplasm and imported in the mitochondria. The control of the mitochondrial proteome by two genomes exposes these organelles to proteotoxic stress in case of an imbalance between the nuclear- and mitochondrial-encoded proteins. Upon such stress, several mitochondrial protein quality control (mtPQC) pathways, including the mitochondrial unfolded protein response (UPRmt), will sense, transmit and re-establish mitochondrial proteostasis through mitonuclear regulatory circuits. Although a robust UPRmt circuit improves health and lifespan in C. elegans, much less is known about mtPQC in vertebrates. We propose here to characterize UPRmt pathways across 3 species by: (1) mapping mammalian UPRmt genes and networks in vivo after the induction of the UPRmt in a large murine genetic reference population at 3 different times throughout life with 2 different inducers; (2) integrating these UPRmt networks with a wide set of clinical, mitochondrial, and molecular phenotypes collected throughout life to establish links between UPRmt mechanisms and health- and lifespan; (3) mechanistically validating the most important UPRmt pathways, using loss-of-function studies in cells, worms and mice; and (4) clinically translating promising UPRmt hits, using genetic association studies in human cohorts. The insight gained will mechanistically define the UPRmt networks from worms to humans and will provide the next step in translating the benefits of activating the UPRmt—initially observed in invertebrates—into targeted human therapies.
Max ERC Funding
2 500 000 €
Duration
Start date: 2018-11-01, End date: 2024-03-31
Project acronym VARB
Project Variability and Robustness in Bio-molecular systems
Researcher (PI) Naama Barkai
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), LS2, ERC-2008-AdG
Summary Cells process information using biochemical networks of interacting proteins and genes. We wish to understand the principles that guide the design of such networks. In particular, we are interested in the interplay between variability, inherent to biological systems, and the precision of cellular computing. To better understand this interplay, we will: (1) Characterize the extent of gene expression variability and define its genetic determinants, (2) Reveal how variability is buffered and (3) Describe instances where variability (or 'noise') is an integral part of cellular computation. The study will be conducted in the multidisciplinary atmosphere of our lab, by students trained in physics, computer science, chemistry and biology. Specific issues include: 1. Gene expression variability: we will focus on the influence of chromatin structure on gene expression variability, as suggested by our bioinformatics analysis. 2. Robustness and scaling in embryonic patterning: We will study the means by which fluctuations are buffered during the development of multicellular organisms. We will focus on the robustness of morphogen gradients to protein levels, and on the ability to maintain proportionate pattern in tissues of different size. 3. Noise-driven transitions in a fluctuating environment: Our preliminary results suggest that noise plays an integral part in phosphate homeostasis in S. cerevisiae. We will characterize the role of noise in this system and study its evolutionary implications. Together, our study will shed light on one we believe to be the fundamental challenge of biological information processing: ensuring a reliable and reproducible function in the highly variable biological environment. Our study will furthermore define novel multidisciplinary, system-level paradigms and approaches that will guide further studies of bio-molecular systems
Summary
Cells process information using biochemical networks of interacting proteins and genes. We wish to understand the principles that guide the design of such networks. In particular, we are interested in the interplay between variability, inherent to biological systems, and the precision of cellular computing. To better understand this interplay, we will: (1) Characterize the extent of gene expression variability and define its genetic determinants, (2) Reveal how variability is buffered and (3) Describe instances where variability (or 'noise') is an integral part of cellular computation. The study will be conducted in the multidisciplinary atmosphere of our lab, by students trained in physics, computer science, chemistry and biology. Specific issues include: 1. Gene expression variability: we will focus on the influence of chromatin structure on gene expression variability, as suggested by our bioinformatics analysis. 2. Robustness and scaling in embryonic patterning: We will study the means by which fluctuations are buffered during the development of multicellular organisms. We will focus on the robustness of morphogen gradients to protein levels, and on the ability to maintain proportionate pattern in tissues of different size. 3. Noise-driven transitions in a fluctuating environment: Our preliminary results suggest that noise plays an integral part in phosphate homeostasis in S. cerevisiae. We will characterize the role of noise in this system and study its evolutionary implications. Together, our study will shed light on one we believe to be the fundamental challenge of biological information processing: ensuring a reliable and reproducible function in the highly variable biological environment. Our study will furthermore define novel multidisciplinary, system-level paradigms and approaches that will guide further studies of bio-molecular systems
Max ERC Funding
2 200 000 €
Duration
Start date: 2009-01-01, End date: 2013-10-31
Project acronym WallWatchers
Project Plant cell wall communication and remodelling: the wall watchers.
Researcher (PI) Julia Santiago Cuellar
Host Institution (HI) UNIVERSITE DE LAUSANNE
Call Details Starting Grant (StG), LS2, ERC-2016-STG
Summary Plants, just like animals are highly developed multicellular organisms. In contrast to animal cells however, plant cells are surrounded by a rigid, carbohydrate-rich extracellular layer, the cell wall. This cell wall provides plants with mechanic support and a dynamic chemical signalling and metabolic environment. To allow for cell expansion, cell division, coordinated tissue growth and interactions with the environment, the cell wall status constantly needs to be sensed and modified. How plant cells perceive and signal their cell wall status is poorly understood. Here, I propose an integrated approach to uncover ligands for cell wall sensing receptors as well as their downstream signalling components. Specifically, my project aims to identify the ligands for two genetically validated cell wall receptor families, using a chemical biology approach. Next, we will analyse and validate the mode of ligand-receptor interaction by combining protein X-ray crystallography, quantitative biochemistry and reverse genetics in Arabidopsis. A detailed ligand-binding and receptor activation mechanism will allow us to specifically interfere with cell wall receptor function in vivo, and to assess their biological relevance for cell wall structure and its chemical properties. Using atomic force microscopy, we will then test if the receptors are distributed uniformly at the membrane or whether they are arranged in complex 'sensosomes'. Finally, we will characterize if plant cell wall receptors can directly act as mechanosensors. With defined receptor-ligand pairs and clear phenotypes at hand, we will try to uncover downstream signalling components for plant cell wall receptors and to validate our atomic models in planta. My ultimate goal would be to design and test cell wall receptor agonists and antagonists, which will represent powerful tools to alter cell wall homoeostasis in Arabidopsis, and potentially in crops.
Summary
Plants, just like animals are highly developed multicellular organisms. In contrast to animal cells however, plant cells are surrounded by a rigid, carbohydrate-rich extracellular layer, the cell wall. This cell wall provides plants with mechanic support and a dynamic chemical signalling and metabolic environment. To allow for cell expansion, cell division, coordinated tissue growth and interactions with the environment, the cell wall status constantly needs to be sensed and modified. How plant cells perceive and signal their cell wall status is poorly understood. Here, I propose an integrated approach to uncover ligands for cell wall sensing receptors as well as their downstream signalling components. Specifically, my project aims to identify the ligands for two genetically validated cell wall receptor families, using a chemical biology approach. Next, we will analyse and validate the mode of ligand-receptor interaction by combining protein X-ray crystallography, quantitative biochemistry and reverse genetics in Arabidopsis. A detailed ligand-binding and receptor activation mechanism will allow us to specifically interfere with cell wall receptor function in vivo, and to assess their biological relevance for cell wall structure and its chemical properties. Using atomic force microscopy, we will then test if the receptors are distributed uniformly at the membrane or whether they are arranged in complex 'sensosomes'. Finally, we will characterize if plant cell wall receptors can directly act as mechanosensors. With defined receptor-ligand pairs and clear phenotypes at hand, we will try to uncover downstream signalling components for plant cell wall receptors and to validate our atomic models in planta. My ultimate goal would be to design and test cell wall receptor agonists and antagonists, which will represent powerful tools to alter cell wall homoeostasis in Arabidopsis, and potentially in crops.
Max ERC Funding
1 499 966 €
Duration
Start date: 2017-07-01, End date: 2022-06-30
Project acronym WHYMIR
Project Interplays between miRNAs and transcription factors in the determination and maintenance of cell identity
Researcher (PI) Mihaiela Luxita Zavolan
Host Institution (HI) UNIVERSITAT BASEL
Call Details Starting Grant (StG), LS2, ERC-2012-StG_20111109
Summary "miRNAs are small RNAs that guide the RNA-induced silencing complex to
mRNA targets, destabilizing them and inhibiting their
translation. Much has been learned about their involvement in organism
development and function, yet some striking puzzles remain. On the one
hand it has been shown that miRNAs are essential for development, and
the preferential targeting of transcription factors (TFs) by miRNAs
suggests that miRNAs and TFs ""coordinate"" to regulate gene
expression. Furthermore, studies in the past year concluded that, on
their own or in combination with TFs, miRNAs can induce reprogramming
of somatic cells into induced pluripotent stem cells (iPSC). On the
other hand, high-throughput measurements of mRNA and protein level
changes upon miRNA transfections suggest that miRNAs have largely a
""fine-tuning"" function. These small effects on individual genes must,
however, confer a substantial selective advantage, because many target
sites remain conserved over long evolutionary distances. Here I first
propose to investigate the hypothesis that instead of primarily
affecting the average levels of target genes, miRNAs reduce the
cell-to-cell variation in gene expression, affecting
precisely the steps that determine the intrinsic noise. I will then
use miRNA-mediated reprogramming of somatic cells into iPSCs as a
model system to directly investigate the ""coordination"" between miRNAs
and TFs in determining cell identity and differentiation. Through
determination of miRNA targets with Argonaute crosslinking and
immunoprecipitation, mRNA sequencing and methylated DNA
immunoprecipitation I attempt to retrace the regulatory interactions
that lead from induction of a few miRNAs, through perturbation of TF
activities, to the activation of ""stemness"" genes. Finally, following
up on preliminary results obtained in my lab, I will investigate the
function of miRNA targeting in the nucleus, that potentially couples
transcriptional and post-transcriptional regulation more directly."
Summary
"miRNAs are small RNAs that guide the RNA-induced silencing complex to
mRNA targets, destabilizing them and inhibiting their
translation. Much has been learned about their involvement in organism
development and function, yet some striking puzzles remain. On the one
hand it has been shown that miRNAs are essential for development, and
the preferential targeting of transcription factors (TFs) by miRNAs
suggests that miRNAs and TFs ""coordinate"" to regulate gene
expression. Furthermore, studies in the past year concluded that, on
their own or in combination with TFs, miRNAs can induce reprogramming
of somatic cells into induced pluripotent stem cells (iPSC). On the
other hand, high-throughput measurements of mRNA and protein level
changes upon miRNA transfections suggest that miRNAs have largely a
""fine-tuning"" function. These small effects on individual genes must,
however, confer a substantial selective advantage, because many target
sites remain conserved over long evolutionary distances. Here I first
propose to investigate the hypothesis that instead of primarily
affecting the average levels of target genes, miRNAs reduce the
cell-to-cell variation in gene expression, affecting
precisely the steps that determine the intrinsic noise. I will then
use miRNA-mediated reprogramming of somatic cells into iPSCs as a
model system to directly investigate the ""coordination"" between miRNAs
and TFs in determining cell identity and differentiation. Through
determination of miRNA targets with Argonaute crosslinking and
immunoprecipitation, mRNA sequencing and methylated DNA
immunoprecipitation I attempt to retrace the regulatory interactions
that lead from induction of a few miRNAs, through perturbation of TF
activities, to the activation of ""stemness"" genes. Finally, following
up on preliminary results obtained in my lab, I will investigate the
function of miRNA targeting in the nucleus, that potentially couples
transcriptional and post-transcriptional regulation more directly."
Max ERC Funding
891 759 €
Duration
Start date: 2012-11-01, End date: 2015-10-31
Project acronym XPRESS
Project Exploring mechanisms of gene repression and escape during X-chromosome inactivation
Researcher (PI) Edith Heard
Host Institution (HI) EUROPEAN MOLECULAR BIOLOGY LABORATORY
Call Details Advanced Grant (AdG), LS2, ERC-2014-ADG
Summary During mammalian development, precise gene expression patterns have to be established and then maintained, or reversed, in different cellular and tissue contexts. A striking example of such developmentally regulated gene control is X-chromosome inactivation (XCI), whereby one of the two X chromosomes in females is silenced during embryogenesis. XCI is initiated by the non-coding Xist RNA, which coats the chromosome in cis, triggering gene repression, chromatin changes and chromosomal reorganisation. Although Xist’s regulation has been investigated intensively, less is known about the actual mechanisms underlying the process of chromosome-wide gene silencing that it induces. Indeed, X-linked loci show very different kinetics of repression during development, implying regional and/or locus specific diversity. Furthermore, some genes avoid or escape XCI altogether, either constitutively or in a tissue or stage-specific fashion, but the molecular basis for this is unclear. Here we propose to dissect the mechanisms underlying gene regulation during XCI. We will investigate the roles of recently identified Xist partners in gene silencing and perform genetic screens to identify new factors involved in silencing and escape from XCI. Transcription, chromatin status and chromosome conformation during XCI will be investigated in an allelic-specific manner during precise developmental time windows to pinpoint the critical changes accompanying silencing and escape. We will use genetic engineering to alter genomic and epigenomic landscapes of selected loci and target candidate trans-acting factors to their putative regulatory elements. Finally, we will develop tools to explore gene expression during XCI using live cell imaging of embryogenesis. Using this innovative set of approaches, we hope to define both general principles underlying gene silencing and escape in XCI, as well as locus-specific features that could serve as new paradigms for research in developmental epigenetics.
Summary
During mammalian development, precise gene expression patterns have to be established and then maintained, or reversed, in different cellular and tissue contexts. A striking example of such developmentally regulated gene control is X-chromosome inactivation (XCI), whereby one of the two X chromosomes in females is silenced during embryogenesis. XCI is initiated by the non-coding Xist RNA, which coats the chromosome in cis, triggering gene repression, chromatin changes and chromosomal reorganisation. Although Xist’s regulation has been investigated intensively, less is known about the actual mechanisms underlying the process of chromosome-wide gene silencing that it induces. Indeed, X-linked loci show very different kinetics of repression during development, implying regional and/or locus specific diversity. Furthermore, some genes avoid or escape XCI altogether, either constitutively or in a tissue or stage-specific fashion, but the molecular basis for this is unclear. Here we propose to dissect the mechanisms underlying gene regulation during XCI. We will investigate the roles of recently identified Xist partners in gene silencing and perform genetic screens to identify new factors involved in silencing and escape from XCI. Transcription, chromatin status and chromosome conformation during XCI will be investigated in an allelic-specific manner during precise developmental time windows to pinpoint the critical changes accompanying silencing and escape. We will use genetic engineering to alter genomic and epigenomic landscapes of selected loci and target candidate trans-acting factors to their putative regulatory elements. Finally, we will develop tools to explore gene expression during XCI using live cell imaging of embryogenesis. Using this innovative set of approaches, we hope to define both general principles underlying gene silencing and escape in XCI, as well as locus-specific features that could serve as new paradigms for research in developmental epigenetics.
Max ERC Funding
2 312 500 €
Duration
Start date: 2015-11-01, End date: 2020-10-31
Project acronym XXDNAM
Project How does the X chromosome regulate DNA methylation in pluripotent stem cells?
Researcher (PI) Steen Kian Thye Ooi
Host Institution (HI) UNIVERSITY COLLEGE LONDON
Call Details Starting Grant (StG), LS2, ERC-2011-StG_20101109
Summary Epigenetic processes regulate gene transcription states during cellular differentiation, playing key roles in the maintenance of pluripotency and differentiation. Epigenetic alterations are common in diseases such as in cancer and cognitive disorders. Understanding the mechanisms by which epigenetic states are inherited and propagated is of fundamental importance, and will help in the development of biomarkers for screening as well identification of targets for disease treatment.
DNA methylation remains the best-characterized epigenetic process. XX pluripotent stem cells (Embryonic Stem (ES) and induced Pluripotent Stem (iPS) cells) display genome-wide hypomethylation relative to XY stem cells but the mechanisms are unknown. This proposal will elucidate the pathways responsible. Irradiation Microcell-Mediated Chromosome Transfer (XMMCT) will be used to identify the critical region(s) of the X chromosome involved. In parallel and as an alternative approach, candidate X-linked genes will be over-expressed in XY ES cells to identify the factors responsible for global hypomethylation. Further insight will be provided using protein interaction screens using epitope-tagged versions of all active Dnmts as well as the known regulators URHF1 and Dnmt3L in XX and XY ES cells. The role of XX-induced hypomethylation in cellular reprogramming will be investigated by using different cell types from Oct4-GFP transgenic mice to examine whether iPS efficiency is affected by cells with a greater propensity to lose DNA methylation. Together these aims will elucidate the signals necessary to maintain global genomic DNA methylation. Aberrant loss is an important hallmark and contributor of disease that could be used for disease diagnosis and treatment. It could also be exploited to help improve the efficiency of cellular reprogramming for regenerative medicine.
Summary
Epigenetic processes regulate gene transcription states during cellular differentiation, playing key roles in the maintenance of pluripotency and differentiation. Epigenetic alterations are common in diseases such as in cancer and cognitive disorders. Understanding the mechanisms by which epigenetic states are inherited and propagated is of fundamental importance, and will help in the development of biomarkers for screening as well identification of targets for disease treatment.
DNA methylation remains the best-characterized epigenetic process. XX pluripotent stem cells (Embryonic Stem (ES) and induced Pluripotent Stem (iPS) cells) display genome-wide hypomethylation relative to XY stem cells but the mechanisms are unknown. This proposal will elucidate the pathways responsible. Irradiation Microcell-Mediated Chromosome Transfer (XMMCT) will be used to identify the critical region(s) of the X chromosome involved. In parallel and as an alternative approach, candidate X-linked genes will be over-expressed in XY ES cells to identify the factors responsible for global hypomethylation. Further insight will be provided using protein interaction screens using epitope-tagged versions of all active Dnmts as well as the known regulators URHF1 and Dnmt3L in XX and XY ES cells. The role of XX-induced hypomethylation in cellular reprogramming will be investigated by using different cell types from Oct4-GFP transgenic mice to examine whether iPS efficiency is affected by cells with a greater propensity to lose DNA methylation. Together these aims will elucidate the signals necessary to maintain global genomic DNA methylation. Aberrant loss is an important hallmark and contributor of disease that could be used for disease diagnosis and treatment. It could also be exploited to help improve the efficiency of cellular reprogramming for regenerative medicine.
Max ERC Funding
1 497 710 €
Duration
Start date: 2011-10-01, End date: 2017-03-31
Project acronym YEASTMEMORY
Project Memory in biological regulatory circuits
Researcher (PI) Kevin Joan Verstrepen
Host Institution (HI) VIB VZW
Call Details Consolidator Grant (CoG), LS2, ERC-2015-CoG
Summary The emergence of intelligence –the ability to remember and analyze data to make decisions– was a milestone in evolution. Intelligence and memory are usually associated with plastic neuronal connections in higher organisms. However, new discoveries hint that a rudimentary form of intelligence is rooted in networks that regulate gene expression in a wide range of organisms, including bacteria and yeasts. Specifically, we and others have shown that microbes show plastic behavioral responses to past experiences, such as previously available nutrients or stresses. This implies that information about the past is somehow retained and passed to next generations, where it influences cellular regulation.
The goal of this project is to use a simple eukaryotic regulatory circuit as a model to obtain a comprehensive picture of the different genes and molecular mechanisms underlying history-dependence (hysteresis) in cellular regulation. Specifically, we will study maltose (MAL) regulation in budding yeast, because this signaling pathway serves as a model for gene regulation circuits in other organisms, including humans. We will use a combination of genetic screens, live-cell microscopy in custom-built microfluidic devices, and mathematical modeling to pursue four aims:
1. To provide a comprehensive quantitative analysis of hysteresis in MAL regulation
2. To unravel the molecular mechanisms contributing to hysteresis
3. To unravel the epigenetic mechanisms allowing hysteresis to extend over several generations
4. To characterize the ecological relevance of hysteresis
This project will establish an innovative model for hysteresis and generate a genome-wide, systems-level view of how past influences can be stored in regulatory cascades to influence cellular decision-making. The results will contribute to a paradigm shift in our view of biological regulation and memory, with possible applications in fields as diverse as industrial microbiology, synthetic biology and medicine.
Summary
The emergence of intelligence –the ability to remember and analyze data to make decisions– was a milestone in evolution. Intelligence and memory are usually associated with plastic neuronal connections in higher organisms. However, new discoveries hint that a rudimentary form of intelligence is rooted in networks that regulate gene expression in a wide range of organisms, including bacteria and yeasts. Specifically, we and others have shown that microbes show plastic behavioral responses to past experiences, such as previously available nutrients or stresses. This implies that information about the past is somehow retained and passed to next generations, where it influences cellular regulation.
The goal of this project is to use a simple eukaryotic regulatory circuit as a model to obtain a comprehensive picture of the different genes and molecular mechanisms underlying history-dependence (hysteresis) in cellular regulation. Specifically, we will study maltose (MAL) regulation in budding yeast, because this signaling pathway serves as a model for gene regulation circuits in other organisms, including humans. We will use a combination of genetic screens, live-cell microscopy in custom-built microfluidic devices, and mathematical modeling to pursue four aims:
1. To provide a comprehensive quantitative analysis of hysteresis in MAL regulation
2. To unravel the molecular mechanisms contributing to hysteresis
3. To unravel the epigenetic mechanisms allowing hysteresis to extend over several generations
4. To characterize the ecological relevance of hysteresis
This project will establish an innovative model for hysteresis and generate a genome-wide, systems-level view of how past influences can be stored in regulatory cascades to influence cellular decision-making. The results will contribute to a paradigm shift in our view of biological regulation and memory, with possible applications in fields as diverse as industrial microbiology, synthetic biology and medicine.
Max ERC Funding
1 959 844 €
Duration
Start date: 2016-10-01, End date: 2021-09-30
Project acronym ZPR
Project The Pancreas Regulome: From causality to prediction of non-coding mutations in human pancreatic diseases
Researcher (PI) José Carlos Ribeiro Bessa
Host Institution (HI) INSTITUTO DE BIOLOGIA MOLECULAR E CELULAR-IBMC
Call Details Starting Grant (StG), LS2, ERC-2015-STG
Summary Several human pancreatic diseases have been characterized, being the diabetes the most common. Like others, this genetic disease is related to disrupted non-coding cis-regulatory elements (CREs) that culminate in altered gene expression. Although Genome Wide Association Studies support this hypothesis, it’s still unclear how mutations on CREs contribute to disease. The translation from the “non-coding code” to phenotype is an exciting and unexplored field that we will approach in this project with the help of the zebrafish as a suitable animal model. We aim to uncover the implications of the disruption of pancreas CREs and how they contribute to diabetes in vivo. For this we will study transcriptional regulation of genes in zebrafish. The similarities between zebrafish and mammal pancreas and the evolutionary conservation of pancreas transcription factors (TF) make it an excellent model to approach and study this disease. In this project we will characterize the zebrafish insulin producing beta-cell regulome, by determining the active CREs in this cell type and their bound TFs. Then we will compare this information with a similar dataset recently available for human beta-cells, to define functional orthologs in these species. Selected CREs will be tested by in vivo gene reporter assays in zebrafish, focusing on those functionally equivalent to human CREs where risk alleles have been associated with diabetes or those regulating genes involved in diabetes. Later these CREs will be mutated in the zebrafish genome to validate their contribution to diabetes. Finally we will translate this to predict new human disease-associated CREs by focusing on the regulatory landscape of diabetes-associated genes, without the need of having countless patients to uncover them. With this project we will create a model system that will allow the identification of new diabetes-associated CREs, which might have a great impact in clinical management of this epidemic disease.
Summary
Several human pancreatic diseases have been characterized, being the diabetes the most common. Like others, this genetic disease is related to disrupted non-coding cis-regulatory elements (CREs) that culminate in altered gene expression. Although Genome Wide Association Studies support this hypothesis, it’s still unclear how mutations on CREs contribute to disease. The translation from the “non-coding code” to phenotype is an exciting and unexplored field that we will approach in this project with the help of the zebrafish as a suitable animal model. We aim to uncover the implications of the disruption of pancreas CREs and how they contribute to diabetes in vivo. For this we will study transcriptional regulation of genes in zebrafish. The similarities between zebrafish and mammal pancreas and the evolutionary conservation of pancreas transcription factors (TF) make it an excellent model to approach and study this disease. In this project we will characterize the zebrafish insulin producing beta-cell regulome, by determining the active CREs in this cell type and their bound TFs. Then we will compare this information with a similar dataset recently available for human beta-cells, to define functional orthologs in these species. Selected CREs will be tested by in vivo gene reporter assays in zebrafish, focusing on those functionally equivalent to human CREs where risk alleles have been associated with diabetes or those regulating genes involved in diabetes. Later these CREs will be mutated in the zebrafish genome to validate their contribution to diabetes. Finally we will translate this to predict new human disease-associated CREs by focusing on the regulatory landscape of diabetes-associated genes, without the need of having countless patients to uncover them. With this project we will create a model system that will allow the identification of new diabetes-associated CREs, which might have a great impact in clinical management of this epidemic disease.
Max ERC Funding
1 497 520 €
Duration
Start date: 2016-06-01, End date: 2021-05-31
