Project acronym BehaEvoDevo
Project Evolution of neuronal cell types, development and circuitry in the insect visual system: breaking down behavioural evolution into its constituent elements
Researcher (PI) Nikolaos Konstantinides
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Country France
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary One of the holy grails of neuroscience is to understand how complex behaviours arise. However, surprisingly little is known about how behaviours evolve. My proposal will delve into Behavioural Evolution and Development (BehaEvoDevo) in an unbiased and comprehensive way using the insect visual system as a model. The visual system of Drosophila has been described extensively in terms of cell type composition, development, circuitry, and behaviour. My expertise in this system will be the springboard to address four fundamental questions: 1) How different is the cell type composition in the brains of different animals? 2) How do the mechanisms that are responsible for neuronal development evolve and how do they affect neuronal diversity? 3) What are the differences in the circuitry that underlies specific behaviours in different animals? 4) How do differences in neuronal composition, neuronal features, or circuitry drive different behaviours? I will combine cutting edge techniques, such as single-cell sequencing, with advanced genetic tools in Drosophila, and adapt innovative tools for genetic manipulation and circuit function in different non-model insects. I will compare how cell type composition, neuronal specification and differentiation, as well as circuitry, affect specific behaviours. I will examine phylogenetically diverse insects to generate a deep understanding of the mechanisms that are most important for the evolution of different behaviours. Moreover, I will identify fundamental principles about how developmental processes, such as neuronal specification and differentiation, evolve to control different behaviours. The cumulative results of this proposal will offer the first comprehensive assessment of the mechanisms that drive evolution of new behaviours across insects; it will also generate a blueprint for the community to compare their data in different clades of the phylogenetic tree as well as to different sensory modalities.
Summary
One of the holy grails of neuroscience is to understand how complex behaviours arise. However, surprisingly little is known about how behaviours evolve. My proposal will delve into Behavioural Evolution and Development (BehaEvoDevo) in an unbiased and comprehensive way using the insect visual system as a model. The visual system of Drosophila has been described extensively in terms of cell type composition, development, circuitry, and behaviour. My expertise in this system will be the springboard to address four fundamental questions: 1) How different is the cell type composition in the brains of different animals? 2) How do the mechanisms that are responsible for neuronal development evolve and how do they affect neuronal diversity? 3) What are the differences in the circuitry that underlies specific behaviours in different animals? 4) How do differences in neuronal composition, neuronal features, or circuitry drive different behaviours? I will combine cutting edge techniques, such as single-cell sequencing, with advanced genetic tools in Drosophila, and adapt innovative tools for genetic manipulation and circuit function in different non-model insects. I will compare how cell type composition, neuronal specification and differentiation, as well as circuitry, affect specific behaviours. I will examine phylogenetically diverse insects to generate a deep understanding of the mechanisms that are most important for the evolution of different behaviours. Moreover, I will identify fundamental principles about how developmental processes, such as neuronal specification and differentiation, evolve to control different behaviours. The cumulative results of this proposal will offer the first comprehensive assessment of the mechanisms that drive evolution of new behaviours across insects; it will also generate a blueprint for the community to compare their data in different clades of the phylogenetic tree as well as to different sensory modalities.
Max ERC Funding
1 632 647 €
Duration
Start date: 2021-09-01, End date: 2026-08-31
Project acronym COSI
Project Understanding organelle communication through contact sites in plant stress responses
Researcher (PI) Inge De Clercq
Host Institution (HI) VIB VZW
Country Belgium
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary To be able to suTo be able to survive constantly changing and often harmful environmental conditions, plants must continuously adapt. Therefore, plants have complex mechanisms that sense and transduce environmental stimuli into adaptive responses. Organelles within the cell are thought to be important sensors and due to their tight integration into whole-cell metabolic and signalling networks, they are in a prime position to communicate stress signals and trigger adaptive responses. However, the mechanisms on how organelles convey stress signals remain poorly understood, especially in plants: “Which is the nature of the signals, how are they propagated and how are they perceived by other organelles?”
I have revealed a novel mechanism how mitochondria, chloroplasts, and the endoplasmic reticulum communicate stress signals to coordinate stress signal transduction into adaptive responses in the nucleus. My recent data provide novel leads that this coordination is mediated by organellar re-positioning and close association with each other. Therefore, I hypothesize that these organelles can associate directly through contact sites to enable fast and efficient communication of stress signals. Although inter-organellar contact sites have been studied in animal and yeast systems, mainly in the context of lipid transfer and calcium exchange, nearly nothing is known on their existence and mode of action in plants.
Understanding the mechanisms and functions of inter-organellar contact sites induced by stress is key in plant stress signalling research. To tackle this question, the COSI project will first identify stress-induced inter-organellar contact sites (SOCS) by means of high-end live-cell imaging and proteomics approaches, followed by their functional characterisation in plant stress responses.
The outcome of COSI is will be a better understanding, and potentially re-evaluation, of the fundamental mechanisms by which plants respond and adapt to stresses.
Summary
To be able to suTo be able to survive constantly changing and often harmful environmental conditions, plants must continuously adapt. Therefore, plants have complex mechanisms that sense and transduce environmental stimuli into adaptive responses. Organelles within the cell are thought to be important sensors and due to their tight integration into whole-cell metabolic and signalling networks, they are in a prime position to communicate stress signals and trigger adaptive responses. However, the mechanisms on how organelles convey stress signals remain poorly understood, especially in plants: “Which is the nature of the signals, how are they propagated and how are they perceived by other organelles?”
I have revealed a novel mechanism how mitochondria, chloroplasts, and the endoplasmic reticulum communicate stress signals to coordinate stress signal transduction into adaptive responses in the nucleus. My recent data provide novel leads that this coordination is mediated by organellar re-positioning and close association with each other. Therefore, I hypothesize that these organelles can associate directly through contact sites to enable fast and efficient communication of stress signals. Although inter-organellar contact sites have been studied in animal and yeast systems, mainly in the context of lipid transfer and calcium exchange, nearly nothing is known on their existence and mode of action in plants.
Understanding the mechanisms and functions of inter-organellar contact sites induced by stress is key in plant stress signalling research. To tackle this question, the COSI project will first identify stress-induced inter-organellar contact sites (SOCS) by means of high-end live-cell imaging and proteomics approaches, followed by their functional characterisation in plant stress responses.
The outcome of COSI is will be a better understanding, and potentially re-evaluation, of the fundamental mechanisms by which plants respond and adapt to stresses.
Max ERC Funding
1 499 327 €
Duration
Start date: 2021-02-01, End date: 2026-01-31
Project acronym EDGE-CAM
Project Edge-based mechanisms coordinating cell wall assembly during plant morphogenesis
Researcher (PI) Charlotte Kirchhelle
Host Institution (HI) INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT
Country France
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary A fundamental question in biology is how multicellular organisms robustly produce organ shapes. The underlying process of morphogenesis involves the integration of biochemical, genetic, and mechanical factors across multiple spatio-temporal scales. In plants, morphogenesis is dominated by the rigid cell wall, which fixes cells in their position. Adjacent cells must therefore coordinate their growth patterns, which are in turn controlled by the mechanical properties of the cell wall. Cell walls are assembled by a complex intracellular trafficking machinery that delivers cell wall components and their associated biosynthetic machinery to different subcellular regions.
Based on our recent discovery that a trafficking route directed to cell edges is essential for cell wall assembly and directional growth at the cell and organ scale, we propose that morphogenesis is controlled by a signalling module at cell edges which integrates feedback from the cell wall. This hypothesis provides a mechanistic explanation for the integration of cell and tissue-level mechanical factors into coordinated cell wall assembly. We propose that a receptor-like protein recently identified as the first known cargo of edge-directed trafficking acts as a core component of a cell wall signalling pathway at edges.
This proposal aims to test our hypothesis through a combination of experimental and computational methods: (1) at the molecular level, we will identify further components of the signalling module through ligand screening, comparative proteomics, and forward genetics; (2) at the cellular level, we will functionally characterise trafficking pathways and their regulation by edge signalling through quantitative imaging, glycomics, and computational mechanics; and (3) at the organ level, we will dissect how robust growth emerges from edge-based feedback on these trafficking pathways. Collectively, these results will provide a multi-scale mechanistic model of morphogenesis in plants.
Summary
A fundamental question in biology is how multicellular organisms robustly produce organ shapes. The underlying process of morphogenesis involves the integration of biochemical, genetic, and mechanical factors across multiple spatio-temporal scales. In plants, morphogenesis is dominated by the rigid cell wall, which fixes cells in their position. Adjacent cells must therefore coordinate their growth patterns, which are in turn controlled by the mechanical properties of the cell wall. Cell walls are assembled by a complex intracellular trafficking machinery that delivers cell wall components and their associated biosynthetic machinery to different subcellular regions.
Based on our recent discovery that a trafficking route directed to cell edges is essential for cell wall assembly and directional growth at the cell and organ scale, we propose that morphogenesis is controlled by a signalling module at cell edges which integrates feedback from the cell wall. This hypothesis provides a mechanistic explanation for the integration of cell and tissue-level mechanical factors into coordinated cell wall assembly. We propose that a receptor-like protein recently identified as the first known cargo of edge-directed trafficking acts as a core component of a cell wall signalling pathway at edges.
This proposal aims to test our hypothesis through a combination of experimental and computational methods: (1) at the molecular level, we will identify further components of the signalling module through ligand screening, comparative proteomics, and forward genetics; (2) at the cellular level, we will functionally characterise trafficking pathways and their regulation by edge signalling through quantitative imaging, glycomics, and computational mechanics; and (3) at the organ level, we will dissect how robust growth emerges from edge-based feedback on these trafficking pathways. Collectively, these results will provide a multi-scale mechanistic model of morphogenesis in plants.
Max ERC Funding
1 499 771 €
Duration
Start date: 2021-09-01, End date: 2026-08-31
Project acronym EnBioSys
Project Energetics of Biological Systems
Researcher (PI) Jonathan Rodenfels
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Country Germany
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary All living systems function out of thermodynamic equilibrium and require a continuous supply of energy. To understand how cells and organisms function, we need to determine how metabolic energy is partitioned among the complex array of cellular processes that are necessary for life at any scale, from isolated biochemical networks to quiescent and highly proliferative cells to organismal growth and development. To investigate the energetics of living systems, I established calorimetry to measure the energy exchanged in the form of heat between biological systems and their environment. By combining these measurements with specific perturbations, I have shown that the energetic costs associated with a given biological process can be calculated, and thus, provides a means towards understanding the energetics of biological systems. This proposal aims to understand the energetic costs of accurate cell signaling, and of homeostasis, proliferation, and growth of cells and organisms. It will further investigate how these biological systems are governed by energetic trade-offs. First, the trade-off between energy dissipation and accuracy of biochemical signaling pathways. Second, the trade-off between power and yield during cell growth and organismal development. Specifically, I will:
1) Develop approaches to quantify the overall energetics of biological systems
2) Elucidate the role of energy dissipation on the accuracy and reproducibility of cell cycle signaling
3) Determine how energetics drive embryonic development and cell growth
This work will overcome the current lack of non-invasive techniques to quantitatively measure metabolic rates, especially rates of energy conversion and dissipation in biological systems. The results will yield quantitative thermodynamic data needed to determine the energetics of biological systems and will be essential for kinetic growth studies of normal and diseased systems.
Summary
All living systems function out of thermodynamic equilibrium and require a continuous supply of energy. To understand how cells and organisms function, we need to determine how metabolic energy is partitioned among the complex array of cellular processes that are necessary for life at any scale, from isolated biochemical networks to quiescent and highly proliferative cells to organismal growth and development. To investigate the energetics of living systems, I established calorimetry to measure the energy exchanged in the form of heat between biological systems and their environment. By combining these measurements with specific perturbations, I have shown that the energetic costs associated with a given biological process can be calculated, and thus, provides a means towards understanding the energetics of biological systems. This proposal aims to understand the energetic costs of accurate cell signaling, and of homeostasis, proliferation, and growth of cells and organisms. It will further investigate how these biological systems are governed by energetic trade-offs. First, the trade-off between energy dissipation and accuracy of biochemical signaling pathways. Second, the trade-off between power and yield during cell growth and organismal development. Specifically, I will:
1) Develop approaches to quantify the overall energetics of biological systems
2) Elucidate the role of energy dissipation on the accuracy and reproducibility of cell cycle signaling
3) Determine how energetics drive embryonic development and cell growth
This work will overcome the current lack of non-invasive techniques to quantitatively measure metabolic rates, especially rates of energy conversion and dissipation in biological systems. The results will yield quantitative thermodynamic data needed to determine the energetics of biological systems and will be essential for kinetic growth studies of normal and diseased systems.
Max ERC Funding
1 935 240 €
Duration
Start date: 2021-04-01, End date: 2026-03-31
Project acronym LIPIDEV
Project Lipid gradients and the dynamics of the plant endomembrane system: from the nano- to the developmental scales
Researcher (PI) Yvon JAILLAIS
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Country France
Call Details Consolidator Grant (CoG), LS3, ERC-2020-COG
Summary Anionic lipids are critical for membrane organization and signaling in eukaryotes, including animals and plants. The dogma is that they accumulate in distinct membranes, thereby recruiting a unique set of lipid-binding proteins to each compartment. In turn, these proteins regulate trafficking and signaling activities on these compartments. However, it is increasingly recognized that anionic lipid distribution is not organelle-specific. In particular, we uncovered the presence of anionic lipids concentration gradients between the membranes of various compartments in plant cells. We further found that these cellular lipid gradients are dynamically regulated during cell differentiation and rapid responses to auxin, one of the major regulators of plant growth and architecture.
Here, we hypothesize that lipid gradients act as a nexus between signaling and trafficking regulations, and thus are critical yet unstudied factors coordinating the very dynamics of the plant endomembrane network.
To test this hypothesis, we will induce controlled fluctuations in anionic lipid gradients to analyze their direct impact on endomembrane morphodynamics, intracellular trafficking and hormone signaling across a broad range of scales ranging from their nano-organization to multicellular development. To do this, we will deploy a portfolio of complementary and innovative approaches, such as optogenetics, subcellular proteomics, and super-resolution live imaging, to visualize and perturb anionic lipids in planta and, for the first time, at relevant spatiotemporal scales.
LIPIDEV represents a complete change of perspective by 1) hypothesizing the importance of lipid gradients in plant cell functions, 2) considering these gradients in their multicellular context, 3) addressing the function of specific lipid pools within cells and tissues, and 4) changing the time scale at which we study anionic lipids, allowing us to dissociate direct and indirect effects associated with these lipids.
Summary
Anionic lipids are critical for membrane organization and signaling in eukaryotes, including animals and plants. The dogma is that they accumulate in distinct membranes, thereby recruiting a unique set of lipid-binding proteins to each compartment. In turn, these proteins regulate trafficking and signaling activities on these compartments. However, it is increasingly recognized that anionic lipid distribution is not organelle-specific. In particular, we uncovered the presence of anionic lipids concentration gradients between the membranes of various compartments in plant cells. We further found that these cellular lipid gradients are dynamically regulated during cell differentiation and rapid responses to auxin, one of the major regulators of plant growth and architecture.
Here, we hypothesize that lipid gradients act as a nexus between signaling and trafficking regulations, and thus are critical yet unstudied factors coordinating the very dynamics of the plant endomembrane network.
To test this hypothesis, we will induce controlled fluctuations in anionic lipid gradients to analyze their direct impact on endomembrane morphodynamics, intracellular trafficking and hormone signaling across a broad range of scales ranging from their nano-organization to multicellular development. To do this, we will deploy a portfolio of complementary and innovative approaches, such as optogenetics, subcellular proteomics, and super-resolution live imaging, to visualize and perturb anionic lipids in planta and, for the first time, at relevant spatiotemporal scales.
LIPIDEV represents a complete change of perspective by 1) hypothesizing the importance of lipid gradients in plant cell functions, 2) considering these gradients in their multicellular context, 3) addressing the function of specific lipid pools within cells and tissues, and 4) changing the time scale at which we study anionic lipids, allowing us to dissociate direct and indirect effects associated with these lipids.
Max ERC Funding
2 374 844 €
Duration
Start date: 2021-10-01, End date: 2026-09-30
Project acronym MOVE_ME
Project Mechanical and Electrical Guidance of Collective Cell Migration in vivo
Researcher (PI) Elias Hernan BARRIGA MANRIQUEZ
Host Institution (HI) FUNDACAO CALOUSTE GULBENKIAN
Country Portugal
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary Directional collective cell migration (dCCM) is key for cellular clusters to reach their target tissues in embryogenesis, tissue repair, and metastasis. Though cells interact with chemical and physical cues when migrating in vivo, the field has mostly focused on studying the chemical guidance (chemotaxis) of dCCM- and the role of physical cues is underappreciated. As chemotaxis is not sufficient to explain dCCM in native contexts, the mechanisms that guide dCCM in vivo remain unclear. Thus, our overall goal is to challenge the classic chemocentric view by addressing whether and how biophysical cues such as mechanical and electrical signals contribute to dCCM in vivo. To tackle this challenging aim, we will study durotaxis (mechanical guidance) and electrotaxis (electrical guidance) at two levels: i) Tissue level, to map mechanical and electrical properties in vivo and test their relative contribution to dCCM and ii) Cellular level, to explore the mechanisms by which cells respond and integrate these biophysical cues. To address this, we will take advantage of the innovative toolbox we developed to study mechanical and electrical cues in vivo. As dCCM occurs in different biological contexts, we propose to generalise our results by studying dCCM of Xenopus neural crest (NCs) in embryogenesis (WP1, WP2), and the migration of the recently discovered Regeneration Organizing Cells (ROCs) in Xenopus tail regeneration (WP3). Demonstrating durotaxis and electrotaxis in vivo has proven to be a challenging goal. Thus, we expect our research to be a breakthrough across fields, bringing new perspectives and tools to study the biophysics of dCCM in vivo for the first time. Finally, this proposal will open new research avenues for my lab and for the field, in which the interplay of biophysical and biochemical cues from the environment could be studied, paving the way to the formulation of a novel and more integrative view of dCCM, and other cell and developmental processes.
Summary
Directional collective cell migration (dCCM) is key for cellular clusters to reach their target tissues in embryogenesis, tissue repair, and metastasis. Though cells interact with chemical and physical cues when migrating in vivo, the field has mostly focused on studying the chemical guidance (chemotaxis) of dCCM- and the role of physical cues is underappreciated. As chemotaxis is not sufficient to explain dCCM in native contexts, the mechanisms that guide dCCM in vivo remain unclear. Thus, our overall goal is to challenge the classic chemocentric view by addressing whether and how biophysical cues such as mechanical and electrical signals contribute to dCCM in vivo. To tackle this challenging aim, we will study durotaxis (mechanical guidance) and electrotaxis (electrical guidance) at two levels: i) Tissue level, to map mechanical and electrical properties in vivo and test their relative contribution to dCCM and ii) Cellular level, to explore the mechanisms by which cells respond and integrate these biophysical cues. To address this, we will take advantage of the innovative toolbox we developed to study mechanical and electrical cues in vivo. As dCCM occurs in different biological contexts, we propose to generalise our results by studying dCCM of Xenopus neural crest (NCs) in embryogenesis (WP1, WP2), and the migration of the recently discovered Regeneration Organizing Cells (ROCs) in Xenopus tail regeneration (WP3). Demonstrating durotaxis and electrotaxis in vivo has proven to be a challenging goal. Thus, we expect our research to be a breakthrough across fields, bringing new perspectives and tools to study the biophysics of dCCM in vivo for the first time. Finally, this proposal will open new research avenues for my lab and for the field, in which the interplay of biophysical and biochemical cues from the environment could be studied, paving the way to the formulation of a novel and more integrative view of dCCM, and other cell and developmental processes.
Max ERC Funding
1 812 125 €
Duration
Start date: 2021-01-01, End date: 2025-12-31
Project acronym NEUROSORTER
Project Uncovering the machinery for the sorting of newly synthesized proteins into the axon
Researcher (PI) Ginny Farias Galdames
Host Institution (HI) UNIVERSITEIT UTRECHT
Country Netherlands
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary Neuronal development and function rely on the polarized distribution of organelles and transmembrane proteins (cargoes) across their somatodendritic and axonal domains. However, it is unknown how organelle organization regulates the polarized sorting of transmembrane proteins to ensure proper neuronal function.
The classical model for sorting of newly synthesized transmembrane proteins to the plasma membrane (PM) follows the biosynthetic pathway via the rough endoplasmic reticulum (ER) and Golgi, which are restricted to the somatodendritic domain in neurons. It is unclear whether this classical secretion pathway is the main route for cargo sorting into the axon or whether an alternative route to the axon is used for most axonal cargoes. Intriguingly, evidence indicates that cargoes can bypass the Golgi for their sorting to the axonal PM. However, the identity of an unconventional secretory pathway has not been demonstrated yet. Here, I propose that selective machinery, including the axonal ER and undefined intermediate compartments, allows local axonal cargo secretion.
Previously, I advanced our knowledge on Golgi-dependent sorting of somatodendritic cargoes and elucidated the mechanisms behind ER organization in neurons. Here, for the first time we will:
1) Identify the sorting routes for newly synthesized axonal proteins
2) Unravel the machinery required for Golgi-independent cargo sorting into the axon, and
3) Elucidate its impact on neuronal development and function
We will use high spatio-temporal resolution imaging and mass-spectrometry combined with novel strategies to control and track cargo secretion, as well as proximity-based labeling to identify key players in the newly identified machinery.
A broad spectrum of human diseases is associated to cargo Golgi-bypass. Neurons offer a unique advantage in spatial resolution to characterize this unconventional route, which could play a key role in human health and disease.
Summary
Neuronal development and function rely on the polarized distribution of organelles and transmembrane proteins (cargoes) across their somatodendritic and axonal domains. However, it is unknown how organelle organization regulates the polarized sorting of transmembrane proteins to ensure proper neuronal function.
The classical model for sorting of newly synthesized transmembrane proteins to the plasma membrane (PM) follows the biosynthetic pathway via the rough endoplasmic reticulum (ER) and Golgi, which are restricted to the somatodendritic domain in neurons. It is unclear whether this classical secretion pathway is the main route for cargo sorting into the axon or whether an alternative route to the axon is used for most axonal cargoes. Intriguingly, evidence indicates that cargoes can bypass the Golgi for their sorting to the axonal PM. However, the identity of an unconventional secretory pathway has not been demonstrated yet. Here, I propose that selective machinery, including the axonal ER and undefined intermediate compartments, allows local axonal cargo secretion.
Previously, I advanced our knowledge on Golgi-dependent sorting of somatodendritic cargoes and elucidated the mechanisms behind ER organization in neurons. Here, for the first time we will:
1) Identify the sorting routes for newly synthesized axonal proteins
2) Unravel the machinery required for Golgi-independent cargo sorting into the axon, and
3) Elucidate its impact on neuronal development and function
We will use high spatio-temporal resolution imaging and mass-spectrometry combined with novel strategies to control and track cargo secretion, as well as proximity-based labeling to identify key players in the newly identified machinery.
A broad spectrum of human diseases is associated to cargo Golgi-bypass. Neurons offer a unique advantage in spatial resolution to characterize this unconventional route, which could play a key role in human health and disease.
Max ERC Funding
1 500 000 €
Duration
Start date: 2020-11-01, End date: 2025-10-31
Project acronym RNAloc
Project Epithelial mRNA localization in homeostasis and pathophysiology
Researcher (PI) Andreas Moor
Host Institution (HI) EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Country Switzerland
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary Asymmetric subcellular mRNA distributions have been observed in a variety of polar cell types and organisms. RNA polarization is instrumental at the beginning of life and determines the morphogen gradients needed for embryo patterning. In highly polar neurons, subcellular transcript localization and translation are thought to enhance cellular efficiency and timely responses to extrinsic cues. However, the functional consequence of mRNA localization has, in most cases, not been elucidated. We have shown that a large fraction of an epithelial transcriptome is localized, yet the role(s) of mRNA localization in adult tissue homeostasis and function are unknown. Moreover, we still do not know how the transcript sorting machinery works, and we lack insights into the molecular composition of the membrane-less compartments that may maintain RNA segregation in the cytoplasm.
We will address these gaps by combining RNA microscopy and subcellular proximity proteomics to study the functional contribution of RNA localization in digestive epithelia. Our project will comprehensively map the subcellular space across three adult epithelial tissues – liver, jejunum, and colon. To elucidate the mechanisms that mediate sequence-specific mRNA transport and maintain localization, we will develop a system to tether a construct for proximity proteomics to localized RNAs. We will functionally test the contribution of RNA localization to tissue homeostasis and disease development by disrupting the localizing elements and machinery.
Our novel toolkit will enable the spatial mapping of RNA and proteins in parallel, allowing us to annotate the subcellular space and subsequently probe the biological significance of this fundamental process in adult epithelia. This novel technology can be extended to the subcellular study of all epithelia and tissues in general; it will ultimately lead to a more comprehensive understanding of tissue function in homeostasis and disease.
Summary
Asymmetric subcellular mRNA distributions have been observed in a variety of polar cell types and organisms. RNA polarization is instrumental at the beginning of life and determines the morphogen gradients needed for embryo patterning. In highly polar neurons, subcellular transcript localization and translation are thought to enhance cellular efficiency and timely responses to extrinsic cues. However, the functional consequence of mRNA localization has, in most cases, not been elucidated. We have shown that a large fraction of an epithelial transcriptome is localized, yet the role(s) of mRNA localization in adult tissue homeostasis and function are unknown. Moreover, we still do not know how the transcript sorting machinery works, and we lack insights into the molecular composition of the membrane-less compartments that may maintain RNA segregation in the cytoplasm.
We will address these gaps by combining RNA microscopy and subcellular proximity proteomics to study the functional contribution of RNA localization in digestive epithelia. Our project will comprehensively map the subcellular space across three adult epithelial tissues – liver, jejunum, and colon. To elucidate the mechanisms that mediate sequence-specific mRNA transport and maintain localization, we will develop a system to tether a construct for proximity proteomics to localized RNAs. We will functionally test the contribution of RNA localization to tissue homeostasis and disease development by disrupting the localizing elements and machinery.
Our novel toolkit will enable the spatial mapping of RNA and proteins in parallel, allowing us to annotate the subcellular space and subsequently probe the biological significance of this fundamental process in adult epithelia. This novel technology can be extended to the subcellular study of all epithelia and tissues in general; it will ultimately lead to a more comprehensive understanding of tissue function in homeostasis and disease.
Max ERC Funding
1 499 984 €
Duration
Start date: 2021-02-01, End date: 2026-01-31
Project acronym TF-Dynamics
Project Illuminating the role of transcription factor dynamics in development
Researcher (PI) Jacques Pierre Bothma
Host Institution (HI) KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Country Netherlands
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary Understanding how genomic regulatory elements encode when and where genes are expressed in development remains one of the most important open questions in biology. Despite intense study, this knowledge gap persists because technological limitations have obscured an important degree of freedom: time. Recent discoveries made with live cell imaging have defied the textbook view of how transcription is regulated. Hence, the time is ripe to introduce a new paradigm for studying transcription in development—one based on how genes are regulated in living animals as development is actually taking place. Excitingly, we can now exploit the cutting-edge live imaging technology and quantitative approaches that I previously developed in order to visualize transcription factor (TF) concentration dynamics, transcription, and even single TF molecules in live Drosophila embryos to uncover how enhancer sequence regulates transcription in vivo. This ambitious work will span multiple length scales, from examining changes in TF concentration at the single-nucleus level, to measuring the formation of local clusters of TFs at the locus level, to watching individual protein-protein interactions as they drive transcription at the molecular level. First, we will understand how TF concentration dynamics regulate gene expression. Second, we will uncover how recently discovered dynamic TF clusters or condensates regulate transcription and how their properties are shaped by enhancer sequence. Finally, we will overcome one of the most daunting technical challenges facing the field of transcription by developing a method to directly visualize the transient protein-protein interactions that drive transcription in vivo. Simultaneously visualizing protein-protein interactions and tracking transcription will make it possible to address the most pressing questions about transcription mechanisms in vivo, by revealing precisely when they occur and how they modulate transcription.
Summary
Understanding how genomic regulatory elements encode when and where genes are expressed in development remains one of the most important open questions in biology. Despite intense study, this knowledge gap persists because technological limitations have obscured an important degree of freedom: time. Recent discoveries made with live cell imaging have defied the textbook view of how transcription is regulated. Hence, the time is ripe to introduce a new paradigm for studying transcription in development—one based on how genes are regulated in living animals as development is actually taking place. Excitingly, we can now exploit the cutting-edge live imaging technology and quantitative approaches that I previously developed in order to visualize transcription factor (TF) concentration dynamics, transcription, and even single TF molecules in live Drosophila embryos to uncover how enhancer sequence regulates transcription in vivo. This ambitious work will span multiple length scales, from examining changes in TF concentration at the single-nucleus level, to measuring the formation of local clusters of TFs at the locus level, to watching individual protein-protein interactions as they drive transcription at the molecular level. First, we will understand how TF concentration dynamics regulate gene expression. Second, we will uncover how recently discovered dynamic TF clusters or condensates regulate transcription and how their properties are shaped by enhancer sequence. Finally, we will overcome one of the most daunting technical challenges facing the field of transcription by developing a method to directly visualize the transient protein-protein interactions that drive transcription in vivo. Simultaneously visualizing protein-protein interactions and tracking transcription will make it possible to address the most pressing questions about transcription mechanisms in vivo, by revealing precisely when they occur and how they modulate transcription.
Max ERC Funding
1 330 400 €
Duration
Start date: 2021-01-01, End date: 2025-12-31
Project acronym ZygoticFate
Project Zygotic Cell Fate and Parent-Biased Gene Expression in Fission Yeast
Researcher (PI) Aleksandar Vjestica
Host Institution (HI) UNIVERSITE DE LAUSANNE
Country Switzerland
Call Details Starting Grant (StG), LS3, ERC-2020-STG
Summary As two gametes fuse, the newly formed zygote immediately represses mating, to prevent polyploid formation, and triggers the developmental program that gives rise to a new individual. My work showed that zygotes of fission yeast and higher eukaryotes bare striking similarities, and here I propose to use this powerful model system to explore the basic mechanisms of gamete-to-zygote transition. Working in fission yeast, where gametes and zygotes are well-defined and accessible to outstanding plethora of experimental approaches, will show how different regulatory mechanisms synergize to execute this key cell fate switch.
Our first aim explores zygotic regulation of gene expression and mating blocks. First, to show how zygote-specific signaling propagates, we will identify its targets using biochemical screens. Second, we will analyse how zygotes alter gene expression. High-throughput sequencing will show transcriptional dynamics and genetics approaches will test its regulation and relevance. Third, we will combine microscopy and genetics to reveal the workings of fungal re-fertilization blocks.
Our second aim explores roles and regulation of the parent-biased allele expression in fungal zygotes that I recently discovered. While biochemical and sequencing-based screens will identify genes asymmetrically expressed from parental genomes, genetics strategies will test their roles. A structural biology workpackage will show how a simple homeodomain transcription factor drives the bias between parental genomes.
Similarities between zygotes of fission yeast and higher eukaryotes hint to the relevance of our work for other developmental systems. By understanding fungal blocks to re-fertilization, which have been previously completely overlooked, we may identify their conserved principles, as increasingly evident for other sexual processes. Finally, exploring the bias in expression of parental alleles in yeast may help explain its recurrence in distant plant and animal lineages.
Summary
As two gametes fuse, the newly formed zygote immediately represses mating, to prevent polyploid formation, and triggers the developmental program that gives rise to a new individual. My work showed that zygotes of fission yeast and higher eukaryotes bare striking similarities, and here I propose to use this powerful model system to explore the basic mechanisms of gamete-to-zygote transition. Working in fission yeast, where gametes and zygotes are well-defined and accessible to outstanding plethora of experimental approaches, will show how different regulatory mechanisms synergize to execute this key cell fate switch.
Our first aim explores zygotic regulation of gene expression and mating blocks. First, to show how zygote-specific signaling propagates, we will identify its targets using biochemical screens. Second, we will analyse how zygotes alter gene expression. High-throughput sequencing will show transcriptional dynamics and genetics approaches will test its regulation and relevance. Third, we will combine microscopy and genetics to reveal the workings of fungal re-fertilization blocks.
Our second aim explores roles and regulation of the parent-biased allele expression in fungal zygotes that I recently discovered. While biochemical and sequencing-based screens will identify genes asymmetrically expressed from parental genomes, genetics strategies will test their roles. A structural biology workpackage will show how a simple homeodomain transcription factor drives the bias between parental genomes.
Similarities between zygotes of fission yeast and higher eukaryotes hint to the relevance of our work for other developmental systems. By understanding fungal blocks to re-fertilization, which have been previously completely overlooked, we may identify their conserved principles, as increasingly evident for other sexual processes. Finally, exploring the bias in expression of parental alleles in yeast may help explain its recurrence in distant plant and animal lineages.
Max ERC Funding
1 702 705 €
Duration
Start date: 2020-12-01, End date: 2025-11-30
