Project acronym DIRNDL
Project Directions in Development
Researcher (PI) Dolf WEIJERS
Host Institution (HI) WAGENINGEN UNIVERSITY
Call Details Advanced Grant (AdG), LS3, ERC-2018-ADG
Summary Cells in multicellular organisms organise along body and tissue axes. Cellular processes, such as division plane orientation, must be aligned with these polarity axes to generate functional 3-dimensional morphology, particularly in plants, where cell walls prevent cell migration. While some polarly localized plant proteins are known, molecular mechanisms of polarity establishment or its translation to division orientation are elusive, in part because regulators in animals and fungi appear to be missing from plant genomes. Cell polarity is first established in the embryo, but this has long been an intractable experimental model. My team has developed the genetic, cell biological and biochemical tools that now render the early Arabidopsis embryo an exquisite model for studying cell polarity and oriented division. Recent efforts already led to the unexpected identification of a novel family of deeply conserved polar plant proteins that share a structural domain with key animal polarity regulators. In the DIRNDL project, we will capitalize upon our unique position and foundational results, and use complementary approaches to discover the plant cell polarity and division orientation system. Firstly, we will address the function of the newly identified conserved polarity proteins, and determine mechanistic convergence of polarity regulators across multicellular kingdoms. Furthermore, we will use proteomic approaches to systematically identify polar proteins, and a genetic approach to identify regulators of polarity and division orientation, essential for embryogenesis. We will functionally analyse polar proteins and regulators both in Arabidopsis and the liverwort Marchantia to help prioritize conserved components, and to facilitate genetic analysis of protein function. Finally, we will use a cell-based system for engineering polarity de novo using the regulators identified in the project, and thus reveal the mechanisms that provide direction in plant development.
Summary
Cells in multicellular organisms organise along body and tissue axes. Cellular processes, such as division plane orientation, must be aligned with these polarity axes to generate functional 3-dimensional morphology, particularly in plants, where cell walls prevent cell migration. While some polarly localized plant proteins are known, molecular mechanisms of polarity establishment or its translation to division orientation are elusive, in part because regulators in animals and fungi appear to be missing from plant genomes. Cell polarity is first established in the embryo, but this has long been an intractable experimental model. My team has developed the genetic, cell biological and biochemical tools that now render the early Arabidopsis embryo an exquisite model for studying cell polarity and oriented division. Recent efforts already led to the unexpected identification of a novel family of deeply conserved polar plant proteins that share a structural domain with key animal polarity regulators. In the DIRNDL project, we will capitalize upon our unique position and foundational results, and use complementary approaches to discover the plant cell polarity and division orientation system. Firstly, we will address the function of the newly identified conserved polarity proteins, and determine mechanistic convergence of polarity regulators across multicellular kingdoms. Furthermore, we will use proteomic approaches to systematically identify polar proteins, and a genetic approach to identify regulators of polarity and division orientation, essential for embryogenesis. We will functionally analyse polar proteins and regulators both in Arabidopsis and the liverwort Marchantia to help prioritize conserved components, and to facilitate genetic analysis of protein function. Finally, we will use a cell-based system for engineering polarity de novo using the regulators identified in the project, and thus reveal the mechanisms that provide direction in plant development.
Max ERC Funding
2 500 000 €
Duration
Start date: 2019-09-01, End date: 2024-08-31
Project acronym DissectPcG
Project Dissecting the Function of Multiple Polycomb Group Complexes in Establishing Transcriptional Identity
Researcher (PI) Diego PASINI
Host Institution (HI) UNIVERSITA DEGLI STUDI DI MILANO
Call Details Consolidator Grant (CoG), LS3, ERC-2016-COG
Summary The activities of the Polycomb group (PcG) of repressive chromatin modifiers are required to maintain correct transcriptional identity during development and differentiation. These activities are altered in a variety of tumours by gain- or loss-of-function mutations, whose mechanistic aspects still remain unclear.
PcGs can be classified in two major repressive complexes (PRC1 and PRC2) with common pathways but distinct biochemical activities. PRC1 catalyses histone H2A ubiquitination of lysine 119, and PRC2 tri-methylation of histone H3 lysine 27. However, PRC1 has a more heterogeneous composition than PRC2, with six mutually exclusive PCGF subunits (PCGF1–6) essential for assembling distinct PRC1 complexes that differ in subunit composition but share the same catalytic core.
While up to six different PRC1 forms can co-exist in a given cell, the molecular mechanisms regulating their activities and their relative contributions to general PRC1 function in any tissue/cell type remain largely unknown. In line with this biochemical heterogeneity, PRC1 retains broader biological functions than PRC2. Critically, however, no molecular analysis has yet been published that dissects the contribution of each PRC1 complex in regulating transcriptional identity.
We will take advantage of newly developed reagents and unpublished genetic models to target each of the six Pcgf genes in either embryonic stem cells or mouse adult tissues. This will systematically dissect the contributions of the different PRC1 complexes to chromatin profiles, gene expression programs, and cellular phenotypes during stem cell self-renewal, differentiation and adult tissue homeostasis. Overall, this will elucidate some of the fundamental mechanisms underlying the establishment and maintenance of cellular identity and will allow us to further determine the molecular links between PcG deregulation and cancer development in a tissue- and/or cell type–specific manner.
Summary
The activities of the Polycomb group (PcG) of repressive chromatin modifiers are required to maintain correct transcriptional identity during development and differentiation. These activities are altered in a variety of tumours by gain- or loss-of-function mutations, whose mechanistic aspects still remain unclear.
PcGs can be classified in two major repressive complexes (PRC1 and PRC2) with common pathways but distinct biochemical activities. PRC1 catalyses histone H2A ubiquitination of lysine 119, and PRC2 tri-methylation of histone H3 lysine 27. However, PRC1 has a more heterogeneous composition than PRC2, with six mutually exclusive PCGF subunits (PCGF1–6) essential for assembling distinct PRC1 complexes that differ in subunit composition but share the same catalytic core.
While up to six different PRC1 forms can co-exist in a given cell, the molecular mechanisms regulating their activities and their relative contributions to general PRC1 function in any tissue/cell type remain largely unknown. In line with this biochemical heterogeneity, PRC1 retains broader biological functions than PRC2. Critically, however, no molecular analysis has yet been published that dissects the contribution of each PRC1 complex in regulating transcriptional identity.
We will take advantage of newly developed reagents and unpublished genetic models to target each of the six Pcgf genes in either embryonic stem cells or mouse adult tissues. This will systematically dissect the contributions of the different PRC1 complexes to chromatin profiles, gene expression programs, and cellular phenotypes during stem cell self-renewal, differentiation and adult tissue homeostasis. Overall, this will elucidate some of the fundamental mechanisms underlying the establishment and maintenance of cellular identity and will allow us to further determine the molecular links between PcG deregulation and cancer development in a tissue- and/or cell type–specific manner.
Max ERC Funding
2 000 000 €
Duration
Start date: 2017-11-01, End date: 2022-10-31
Project acronym DIVIMAGE
Project Bridging spatial and temporal resolution gaps in the study of cell division
Researcher (PI) Daniel Wolfram Gerlich
Host Institution (HI) INSTITUT FUER MOLEKULARE BIOTECHNOLOGIE GMBH
Call Details Starting Grant (StG), LS3, ERC-2011-StG_20101109
Summary Cell division underlies the growth and development of all living organisms. Following partitioning of bulk cytoplasmic contents by cleavage furrow ingression, dividing animal cells split by a distinct process termed abscission. Whereas a number of factors required for abscission have been identified in previous studies, it is not known by which mechanism they mediate fission of the intercellular bridge between the nascent sister cells. Here, we will establish correlative workflows of time-lapse imaging, super resolution fluorescence microscopy, electron tomography, and electrophysiological assays to bridge spatial and temporal resolution gaps in the study of abscission. We will further develop computational tools for image-based RNAi screening. With this, we aim to:
1) elucidate how membrane and cytoskeletal dynamics coordinately split the intercellular bridge;
2) uncover the signaling pathways controlling abscission timing.
Failure in abscission can lead to aneuploidy and cancer. Elucidating its mechanism and temporal control is therefore of general biological and medical relevance. The computational and correlative imaging methods developed in this project will further provide the research community new possibilities for mechanistic studies in intact cells.
Summary
Cell division underlies the growth and development of all living organisms. Following partitioning of bulk cytoplasmic contents by cleavage furrow ingression, dividing animal cells split by a distinct process termed abscission. Whereas a number of factors required for abscission have been identified in previous studies, it is not known by which mechanism they mediate fission of the intercellular bridge between the nascent sister cells. Here, we will establish correlative workflows of time-lapse imaging, super resolution fluorescence microscopy, electron tomography, and electrophysiological assays to bridge spatial and temporal resolution gaps in the study of abscission. We will further develop computational tools for image-based RNAi screening. With this, we aim to:
1) elucidate how membrane and cytoskeletal dynamics coordinately split the intercellular bridge;
2) uncover the signaling pathways controlling abscission timing.
Failure in abscission can lead to aneuploidy and cancer. Elucidating its mechanism and temporal control is therefore of general biological and medical relevance. The computational and correlative imaging methods developed in this project will further provide the research community new possibilities for mechanistic studies in intact cells.
Max ERC Funding
1 500 000 €
Duration
Start date: 2012-03-01, End date: 2017-02-28
Project acronym DIVISIONPLANESWITCH
Project Control mechanisms that pattern microtubules for switching cell division planes during plant morphogenesis
Researcher (PI) Pankaj Bacharam Dhonukshe
Host Institution (HI) VIB VZW
Call Details Starting Grant (StG), LS3, ERC-2012-StG_20111109
Summary Oriented cell divisions dictate morphogenesis by shaping tissues and organs of multicellular organisms. Oriented cell divisions have profound influence in plants because their cell positions are locked by shared cell walls. A relay of cell divisions involving precise division plane switches determines embryonic body plan, organ layout and organ architecture in plants. Cell division planes in plants are specified by reorganization of premitotic cortical microtubule array and how this occurs is a long-standing key question.
My recent results establish, for the first time in plants, an in vivo inducible and traceable, precise 90º cell division plane switch system. With this system I identified a pathway that proceeds from transcriptional activation through a signaling module all the way to the activation of microtubule regulators that orchestrate switches in premitotic microtubule organization and cell division planes. My findings provide a first paradigm in plants of how genetic circuitry patterns cell division planes via feeding onto cellular machinery and pave the way for unraveling mechanistic control of cell division plane switch.
By establishing a precise cell division plane switch system I am in a unique position to answer:
1. What transcriptional program and molecular players control premitotic microtubule reorganization?
2. Which mechanisms switch premitotic microtubule array?
3. What influence do identified players and mechanisms have on different types of oriented cell divisions in plants?
For this I propose a systematic research plan combining (i) forward genetics and expression profile screens for identifying a suite of microtubule regulators, (ii) state-of-the-art microscopy and modeling approaches for uncovering mechanisms of their actions and (iii) their tissue-specific manipulations to modify plant form.
By unraveling players and mechanisms this proposal shall resolve regulation of oriented cell divisions and expand plant engineering toolbox.
Summary
Oriented cell divisions dictate morphogenesis by shaping tissues and organs of multicellular organisms. Oriented cell divisions have profound influence in plants because their cell positions are locked by shared cell walls. A relay of cell divisions involving precise division plane switches determines embryonic body plan, organ layout and organ architecture in plants. Cell division planes in plants are specified by reorganization of premitotic cortical microtubule array and how this occurs is a long-standing key question.
My recent results establish, for the first time in plants, an in vivo inducible and traceable, precise 90º cell division plane switch system. With this system I identified a pathway that proceeds from transcriptional activation through a signaling module all the way to the activation of microtubule regulators that orchestrate switches in premitotic microtubule organization and cell division planes. My findings provide a first paradigm in plants of how genetic circuitry patterns cell division planes via feeding onto cellular machinery and pave the way for unraveling mechanistic control of cell division plane switch.
By establishing a precise cell division plane switch system I am in a unique position to answer:
1. What transcriptional program and molecular players control premitotic microtubule reorganization?
2. Which mechanisms switch premitotic microtubule array?
3. What influence do identified players and mechanisms have on different types of oriented cell divisions in plants?
For this I propose a systematic research plan combining (i) forward genetics and expression profile screens for identifying a suite of microtubule regulators, (ii) state-of-the-art microscopy and modeling approaches for uncovering mechanisms of their actions and (iii) their tissue-specific manipulations to modify plant form.
By unraveling players and mechanisms this proposal shall resolve regulation of oriented cell divisions and expand plant engineering toolbox.
Max ERC Funding
1 500 000 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym DNADEMETHYLASE
Project Functions and mechanism of active DNA demethylation
Researcher (PI) Heinz Christof Niehrs
Host Institution (HI) INSTITUT FUR MOLEKULARE BIOLOGIE GGMBH
Call Details Advanced Grant (AdG), LS3, ERC-2009-AdG
Summary Epigenetic gene regulation is of central importance for development and disease. Despite dramatic progress in epigenetics during the past decade, DNA demethylation remains one of the last big frontiers and very little is known about it. DNA demethylation is a widespread phenomenon and occurs in plants as well as in animals, during development, in the adult, and during somatic cell reprogramming of pluripotency genes. The molecular identity of the DNA demethylase in animal cells remained unresolved and has hampered progress in the field for decades. In 2007 we published that Growth Arrest and DNA Damage 45 a (Gadd45a) is a key player in active DNA demethylation, which opened new avenues in the study of this elusive process. The goal of this project is to further analyze the mechanism of DNA demethylation as well as the role played by Gadd45 in development. Given the many unresolved questions in this burgeoning field, our work promises to be ground-breaking and therefore have a profound impact in unraveling one of the least understood processes of gene regulation. Specifically we will address the following points. I) The biological role of Gadd45 mediated DNA demethylation in mouse embryos and adults is unknown. We have obtained mouse mutants for Gadd45a,b, and g and we will analyze them for developmental defects and dissect the methylation regulation of relevant genes. II) The targeting mechanism by which Gadd45 is binding to and demethylating specific sites in the genome is a central unresolved issue. We have identified a candidate DNA binding protein interacting with Gadd45 and we will analyze its role in site specific targeting of DNA demethylation in vitro and in mouse. III) We found that Gadd45 is an RNA binding protein and we will therefore analyze how non-coding RNAs are involved in targeting and/or activating Gadd45 during DNA demethylation.
Summary
Epigenetic gene regulation is of central importance for development and disease. Despite dramatic progress in epigenetics during the past decade, DNA demethylation remains one of the last big frontiers and very little is known about it. DNA demethylation is a widespread phenomenon and occurs in plants as well as in animals, during development, in the adult, and during somatic cell reprogramming of pluripotency genes. The molecular identity of the DNA demethylase in animal cells remained unresolved and has hampered progress in the field for decades. In 2007 we published that Growth Arrest and DNA Damage 45 a (Gadd45a) is a key player in active DNA demethylation, which opened new avenues in the study of this elusive process. The goal of this project is to further analyze the mechanism of DNA demethylation as well as the role played by Gadd45 in development. Given the many unresolved questions in this burgeoning field, our work promises to be ground-breaking and therefore have a profound impact in unraveling one of the least understood processes of gene regulation. Specifically we will address the following points. I) The biological role of Gadd45 mediated DNA demethylation in mouse embryos and adults is unknown. We have obtained mouse mutants for Gadd45a,b, and g and we will analyze them for developmental defects and dissect the methylation regulation of relevant genes. II) The targeting mechanism by which Gadd45 is binding to and demethylating specific sites in the genome is a central unresolved issue. We have identified a candidate DNA binding protein interacting with Gadd45 and we will analyze its role in site specific targeting of DNA demethylation in vitro and in mouse. III) We found that Gadd45 is an RNA binding protein and we will therefore analyze how non-coding RNAs are involved in targeting and/or activating Gadd45 during DNA demethylation.
Max ERC Funding
2 376 000 €
Duration
Start date: 2010-06-01, End date: 2015-05-31
Project acronym DOME
Project Dissecting a Novel Mechanism of Cell Motility
Researcher (PI) Tâm Mignot
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), LS3, ERC-2010-StG_20091118
Summary Cell motility is essential for many biological processes, including development and pathogenesis. Thus, the
molecular mechanisms underlying this process have been intensively studied in many cell systems, for
example, leukocytes, amoeba and even bacteria. Intriguingly, bacteria are also able to move across solid
surfaces (gliding motility) like eukaryotic cells by a process that has remained largely mysterious. The
emergence of bacterial cell biology: the discovery that the bacterial cell also has a dynamic cytoskeleton and
specialized subcellular regions now provides new research angles to study the motility mechanism. Using
cell biology approaches, we previously suggested that the mechanism may be akin to acto-myosin-based
motility in eukaryotic cells and proposed that bacterial focal adhesion complexes also power locomotion. In
this project, we propose two complementary research axes to define both the mechanism and its spatial
regulation in the cell at molecular resolution.
Using the model motility bacterium Myxococcus xanthus, we first propose to develop a “toolbox” of
biophysical and cell biology assays to analyze the motility process. Specifically, we will construct a Traction
Force Microscopy assay designed to image the motility forces directly by live moving cells and use
microfluidics to quantitate the secretion of a mucus that may participate directly in the motility process.
These assays, combined with a newly developed laser trap system to visualize dynamic focal adhesions in
the cell envelope, will be instrumental not only to define new features of the motility process, but also to
study the function of novel motility genes which may encode the components of the elusive motility engine.
This way, we hope to establish the mechanism and structure function relationships within an entirely novel
motility machinery.
In a second part, we propose to investigate the mechanism that controls a polarity switch, allowing M.
xanthus cells to change their direction of movement. We have previously shown that dynamic motility
protein pole-to-pole oscillations convert the initial leading cell pole into the lagging pole. Here, we propose
that like in a eukaryotic cells, a bacterial counterpart of small GTPases of the Ras superfamily, MglA
controls the polarity cycle. To test this hypothesis, we will study both the MglA upstream regulation and the
MglA downstream effectors. We thus hope to establish a model of dynamic polarity control in a bacterial
Summary
Cell motility is essential for many biological processes, including development and pathogenesis. Thus, the
molecular mechanisms underlying this process have been intensively studied in many cell systems, for
example, leukocytes, amoeba and even bacteria. Intriguingly, bacteria are also able to move across solid
surfaces (gliding motility) like eukaryotic cells by a process that has remained largely mysterious. The
emergence of bacterial cell biology: the discovery that the bacterial cell also has a dynamic cytoskeleton and
specialized subcellular regions now provides new research angles to study the motility mechanism. Using
cell biology approaches, we previously suggested that the mechanism may be akin to acto-myosin-based
motility in eukaryotic cells and proposed that bacterial focal adhesion complexes also power locomotion. In
this project, we propose two complementary research axes to define both the mechanism and its spatial
regulation in the cell at molecular resolution.
Using the model motility bacterium Myxococcus xanthus, we first propose to develop a “toolbox” of
biophysical and cell biology assays to analyze the motility process. Specifically, we will construct a Traction
Force Microscopy assay designed to image the motility forces directly by live moving cells and use
microfluidics to quantitate the secretion of a mucus that may participate directly in the motility process.
These assays, combined with a newly developed laser trap system to visualize dynamic focal adhesions in
the cell envelope, will be instrumental not only to define new features of the motility process, but also to
study the function of novel motility genes which may encode the components of the elusive motility engine.
This way, we hope to establish the mechanism and structure function relationships within an entirely novel
motility machinery.
In a second part, we propose to investigate the mechanism that controls a polarity switch, allowing M.
xanthus cells to change their direction of movement. We have previously shown that dynamic motility
protein pole-to-pole oscillations convert the initial leading cell pole into the lagging pole. Here, we propose
that like in a eukaryotic cells, a bacterial counterpart of small GTPases of the Ras superfamily, MglA
controls the polarity cycle. To test this hypothesis, we will study both the MglA upstream regulation and the
MglA downstream effectors. We thus hope to establish a model of dynamic polarity control in a bacterial
Max ERC Funding
1 437 693 €
Duration
Start date: 2011-01-01, End date: 2015-12-31
Project acronym DORMANTOOCYTE
Project Understanding the Balbiani body: A super-organelle linked to dormancy in oocytes
Researcher (PI) Elvan Boke
Host Institution (HI) FUNDACIO CENTRE DE REGULACIO GENOMICA
Call Details Starting Grant (StG), LS3, ERC-2017-STG
Summary Female germ cells, oocytes, are highly specialised cells. They ensure the continuity of species by providing the female genome and mitochondria along with most of the nutrients and housekeeping machinery the early embryo needs after fertilisation. Oocytes are remarkable in their ability to survive for long periods of time, up to 50 years in humans, and retain the ability to give rise to a young organism while other cells age and die. Surprisingly little is known about oocyte dormancy. A key feature of dormant oocytes of virtually all vertebrates is the presence of a Balbiani body, which is a non-membrane bound compartment that contains most of the organelles in dormant oocytes and disappears as the oocyte matures.
The goal of this proposal is to combine genetic and biochemical perturbations with imaging and the state of the art proteomics techniques to reveal the mechanisms dormant oocytes employ to remain viable. My previous research has shown that the Balbiani body forms an amyloid-like cage around organelles that could be protective. This has led me to identify the large number of unanswered questions about the cell biology of a dormant oocyte. In this proposal, we will study three of these questions: 1) What is the metabolic nature of organelles in dormant oocytes? 2) How does the Balbiani body disassemble and release the complement of organelles when oocytes start to mature? 3) What is the structure and function of the Balbiani body in mammals? We will use oocytes from two vertebrate species, frogs and mice, which are complementary for their ease of handling and relationship to human physiology.
By studying the Balbiani body, this proposal will provide fundamental insights into organisation and function of organelles in oocytes and the regulation of physiological amyloid-like structures. More generally, the proposed experiments open up new avenues into the mechanisms that protect organelles from ageing and how oocytes stay dormant for many decades.
Summary
Female germ cells, oocytes, are highly specialised cells. They ensure the continuity of species by providing the female genome and mitochondria along with most of the nutrients and housekeeping machinery the early embryo needs after fertilisation. Oocytes are remarkable in their ability to survive for long periods of time, up to 50 years in humans, and retain the ability to give rise to a young organism while other cells age and die. Surprisingly little is known about oocyte dormancy. A key feature of dormant oocytes of virtually all vertebrates is the presence of a Balbiani body, which is a non-membrane bound compartment that contains most of the organelles in dormant oocytes and disappears as the oocyte matures.
The goal of this proposal is to combine genetic and biochemical perturbations with imaging and the state of the art proteomics techniques to reveal the mechanisms dormant oocytes employ to remain viable. My previous research has shown that the Balbiani body forms an amyloid-like cage around organelles that could be protective. This has led me to identify the large number of unanswered questions about the cell biology of a dormant oocyte. In this proposal, we will study three of these questions: 1) What is the metabolic nature of organelles in dormant oocytes? 2) How does the Balbiani body disassemble and release the complement of organelles when oocytes start to mature? 3) What is the structure and function of the Balbiani body in mammals? We will use oocytes from two vertebrate species, frogs and mice, which are complementary for their ease of handling and relationship to human physiology.
By studying the Balbiani body, this proposal will provide fundamental insights into organisation and function of organelles in oocytes and the regulation of physiological amyloid-like structures. More generally, the proposed experiments open up new avenues into the mechanisms that protect organelles from ageing and how oocytes stay dormant for many decades.
Max ERC Funding
1 381 286 €
Duration
Start date: 2018-03-01, End date: 2023-02-28
Project acronym DROPFAT
Project Biogenesis of lipid droplets and lipid homeostasis
Researcher (PI) Pedro Nuno Chaves Simoes De Carvalho
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Call Details Starting Grant (StG), LS3, ERC-2012-StG_20111109
Summary Organisms and cells face a myriad of environmental changes with periods of nutrient surplus and shortage. It is therefore not surprising that in all kingdoms of life, cells have evolved the means to store energy and thereby minimize the effects of environmental fluctuations. While the capability for energy storage has obvious advantages, deregulated energy accumulation can also be detrimental and is the hallmark of many diseases such as obesity.
In most cells energy is stored as neutral lipids in a dedicated cellular compartment, the lipid droplets (LDs). LDs are found in virtually every eukaryotic cell and play a central role in cellular lipid and energy metabolism. Despite their ubiquitous presence and importance, the physiology of LDs is poorly understood. LDs are composed of a single lipid layer and therefore distinct from all other cellular compartments. How do LDs originate at the endoplasmic reticulum (ER) and what is the machinery involved? How is the size, number and the storage capacity of the LDs regulated? How are specific proteins and lipids targeted to LDs? Addressing these questions is fundamental for understanding the “life cycle” of LDs and for a global picture of the cellular energy homeostasis.
The main goal of this proposal is to reveal the molecular mechanisms controlling neutral lipid dynamics and their storage in LDs. We will focus specifically on the role of the endoplasmic reticulum in the biogenesis of LDs. First, we will identify the ER protein complexes required for LD formation and regulation. Second, we will develop an assay to dissect the targeting of proteins to LDs. Finally, we will develop a cell-free system that recapitulates the biogenesis of LDs in vitro. Altogether, our strategy constitutes a systematic, in-depth analysis of LD dynamics and will lead to significant insight on the mechanisms of cellular energy storage. Our findings will likely offer a better understanding of human pathologies such as obesity and lipodistrophies
Summary
Organisms and cells face a myriad of environmental changes with periods of nutrient surplus and shortage. It is therefore not surprising that in all kingdoms of life, cells have evolved the means to store energy and thereby minimize the effects of environmental fluctuations. While the capability for energy storage has obvious advantages, deregulated energy accumulation can also be detrimental and is the hallmark of many diseases such as obesity.
In most cells energy is stored as neutral lipids in a dedicated cellular compartment, the lipid droplets (LDs). LDs are found in virtually every eukaryotic cell and play a central role in cellular lipid and energy metabolism. Despite their ubiquitous presence and importance, the physiology of LDs is poorly understood. LDs are composed of a single lipid layer and therefore distinct from all other cellular compartments. How do LDs originate at the endoplasmic reticulum (ER) and what is the machinery involved? How is the size, number and the storage capacity of the LDs regulated? How are specific proteins and lipids targeted to LDs? Addressing these questions is fundamental for understanding the “life cycle” of LDs and for a global picture of the cellular energy homeostasis.
The main goal of this proposal is to reveal the molecular mechanisms controlling neutral lipid dynamics and their storage in LDs. We will focus specifically on the role of the endoplasmic reticulum in the biogenesis of LDs. First, we will identify the ER protein complexes required for LD formation and regulation. Second, we will develop an assay to dissect the targeting of proteins to LDs. Finally, we will develop a cell-free system that recapitulates the biogenesis of LDs in vitro. Altogether, our strategy constitutes a systematic, in-depth analysis of LD dynamics and will lead to significant insight on the mechanisms of cellular energy storage. Our findings will likely offer a better understanding of human pathologies such as obesity and lipodistrophies
Max ERC Funding
1 475 282 €
Duration
Start date: 2013-02-01, End date: 2018-01-31
Project acronym DROSOPHILASIGNALING
Project Signaling Pathways Controlling Patterning, Growth and Final Size of Drosophila Limbs
Researcher (PI) Konrad Basler
Host Institution (HI) UNIVERSITAT ZURICH
Call Details Advanced Grant (AdG), LS3, ERC-2008-AdG
Summary Developmental biology seeks not only to learn more about the fundamental processes of growth and pattern per se, but to understand how they synergize to enable the morphogenesis of multicellular organisms. Our goal is to perform real-time analyses of these developmental processes in an intact developing organ. By applying a vital imaging approach, we can circumvent the normal limitations of inferring cellular dynamics from static images or molecular data, and obtain the real dynamic view of growth and patterning. The wing imaginal disc of Drosophila, which starts out as a simple epithelial structure and gives rise to a precisely structured adult limb, will serve as an ideal model system. This system has the combined advantages of relative simplicity and genetic tractability. We will create several innovations that expand the current toolkit and thus facilitate the detailed dissection of growth and patterning. A key early step will be to develop novel reporters to dynamically and faithfully monitor signaling cascades involved in growth and patterning, such as the Dpp and Hippo pathways. We will also implement quantification techniques that are currently being set up in collaboration with an experimental physicist, to deduce, and alter, the mechanical forces that develop in the cells of a growing tissue. The large amount of quantitative data that will be generated allow us derive computational models of the individual pathways and their interaction. The focus of the study will be to answer the following questions: 1) Is the Hippo pathway regulated spatially and temporally, and by what signaling pathways? 2) Do mechanical forces play a pivotal controlling role in organ morphogenesis? 3) What are the global effects on growth, when pathways controlling patterning, cell competition or compensatory proliferation are perturbed? The proposed project will bring the approaches taken to define the mechanisms underlying and controlling growth and patterning to the next level.
Summary
Developmental biology seeks not only to learn more about the fundamental processes of growth and pattern per se, but to understand how they synergize to enable the morphogenesis of multicellular organisms. Our goal is to perform real-time analyses of these developmental processes in an intact developing organ. By applying a vital imaging approach, we can circumvent the normal limitations of inferring cellular dynamics from static images or molecular data, and obtain the real dynamic view of growth and patterning. The wing imaginal disc of Drosophila, which starts out as a simple epithelial structure and gives rise to a precisely structured adult limb, will serve as an ideal model system. This system has the combined advantages of relative simplicity and genetic tractability. We will create several innovations that expand the current toolkit and thus facilitate the detailed dissection of growth and patterning. A key early step will be to develop novel reporters to dynamically and faithfully monitor signaling cascades involved in growth and patterning, such as the Dpp and Hippo pathways. We will also implement quantification techniques that are currently being set up in collaboration with an experimental physicist, to deduce, and alter, the mechanical forces that develop in the cells of a growing tissue. The large amount of quantitative data that will be generated allow us derive computational models of the individual pathways and their interaction. The focus of the study will be to answer the following questions: 1) Is the Hippo pathway regulated spatially and temporally, and by what signaling pathways? 2) Do mechanical forces play a pivotal controlling role in organ morphogenesis? 3) What are the global effects on growth, when pathways controlling patterning, cell competition or compensatory proliferation are perturbed? The proposed project will bring the approaches taken to define the mechanisms underlying and controlling growth and patterning to the next level.
Max ERC Funding
2 310 000 €
Duration
Start date: 2009-02-01, End date: 2014-01-31
Project acronym DROSOPIRNAS
Project The piRNA pathway in the Drosophila germline a small RNA based genome immune system
Researcher (PI) Julius Brennecke
Host Institution (HI) INSTITUT FUER MOLEKULARE BIOTECHNOLOGIE GMBH
Call Details Starting Grant (StG), LS3, ERC-2010-StG_20091118
Summary The discovery of RNA interference (RNAi) has revolutionized biology. As a technology it opened up new experimental and therapeutic avenues. As a biological phenomenon it changed our view on a diverse array of cellular processes. Among those are the control of gene expression, the suppression of viral replication, the formation of heterochromatin and the protection of the genome against selfish genetic elements such as transposons.
I propose to study the molecular mechanism and the biological impact of a recently discovered RNAi pathway, the Piwi interacting RNA pathway (piRNA pathway).
The piRNA pathway is an evolutionarily conserved small RNA pathway acting in the animal germline. It is the key genome surveillance system that suppresses the activity of transposons. Recent work has provided a conceptual framework for this pathway: According to this, the genome stores transposon sequences in heterochromatic loci called piRNA clusters. These provide the RNA substrates for the biogenesis of 23-29 nt long piRNAs. An amplification cycle steers piRNA production predominantly to those cluster regions that are complementary to transposons being active at a given time. Finally, piRNAs guide a protein complex centered on Piwi-proteins to complementary transposon RNAs in the cell, leading to their silencing.
In contrast to other RNAi pathways, the mechanistic framework of the piRNA pathway is largely unknown. Moreover, the spectrum of biological processes impacted by it is only poorly understood. piRNAs are for example not only derived from transposon sequences but also from various other genomic repeats that are enriched at telomeres and in heterochromatin.
We will systematically dissect the piRNA pathway regarding its molecular architecture as well as its biological functions in Drosophila. Our studies will be a combination of fly genetics, proteomics and genomics approaches. Throughout we aim at linking our results back to the underlying biology of germline development.
Summary
The discovery of RNA interference (RNAi) has revolutionized biology. As a technology it opened up new experimental and therapeutic avenues. As a biological phenomenon it changed our view on a diverse array of cellular processes. Among those are the control of gene expression, the suppression of viral replication, the formation of heterochromatin and the protection of the genome against selfish genetic elements such as transposons.
I propose to study the molecular mechanism and the biological impact of a recently discovered RNAi pathway, the Piwi interacting RNA pathway (piRNA pathway).
The piRNA pathway is an evolutionarily conserved small RNA pathway acting in the animal germline. It is the key genome surveillance system that suppresses the activity of transposons. Recent work has provided a conceptual framework for this pathway: According to this, the genome stores transposon sequences in heterochromatic loci called piRNA clusters. These provide the RNA substrates for the biogenesis of 23-29 nt long piRNAs. An amplification cycle steers piRNA production predominantly to those cluster regions that are complementary to transposons being active at a given time. Finally, piRNAs guide a protein complex centered on Piwi-proteins to complementary transposon RNAs in the cell, leading to their silencing.
In contrast to other RNAi pathways, the mechanistic framework of the piRNA pathway is largely unknown. Moreover, the spectrum of biological processes impacted by it is only poorly understood. piRNAs are for example not only derived from transposon sequences but also from various other genomic repeats that are enriched at telomeres and in heterochromatin.
We will systematically dissect the piRNA pathway regarding its molecular architecture as well as its biological functions in Drosophila. Our studies will be a combination of fly genetics, proteomics and genomics approaches. Throughout we aim at linking our results back to the underlying biology of germline development.
Max ERC Funding
1 500 000 €
Duration
Start date: 2010-09-01, End date: 2015-08-31
