Gilles Charvin

Gilles Charvin
Institut de Génétique et de Biologie Moléculaire et Cellulaire | IGBMC · Department of Biology and Stem Cell Development

PhD

About

97
Publications
8,510
Reads
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2,174
Citations
Additional affiliations
January 2011 - present
Institut de Génétique et de Biologie Moléculaire et Cellulaire
Position
  • Group Leader
October 2008 - December 2010
Ecole normale supérieure de Lyon
Position
  • Researcher
January 2005 - October 2008
The Rockefeller University
Position
  • PostDoc Position

Publications

Publications (97)
Article
Full-text available
Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. So far, strong limitations in the ability to quantitatively analyze single-cell trajectories have prevented large-scale investigations to assess the dynamics of entry into repl...
Article
Microorganisms have evolved adaptive strategies to respond to the autonomous degradation of their environment. Indeed, a growing culture progressively exhausts nutrients from its media and modifies its composition. Yet, how single cells react to these modifications remains difficult to study since it requires population-scale growth experiments to...
Article
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin-associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex,...
Article
Full-text available
The nuclear pore complex (NPC) mediates nearly all exchanges between nucleus and cytoplasm, and in many species it changes composition as the organism ages. However, how these changes arise and whether they contribute themselves to ageing is poorly understood. We show that SAGA-dependent attachment of DNA circles to NPCs in replicatively ageing yea...
Article
Full-text available
The life cycle of microorganisms is associated with dynamic metabolic transitions and complex cellular responses. In yeast, how metabolic signals control the progressive choreography of structural reorganizations observed in quiescent cells during a natural life cycle remains unclear. We have developed an integrated microfluidic device to address t...
Preprint
Full-text available
Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. Here, we have developed DetecDiv, a microfluidic-based image acquisition platform combined with deep learning-based software for high-throughput single-cell division tracking....
Preprint
Full-text available
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm and regulate gene expression by interacting with transcription and mRNA export factors. We find that Esa1, the catalytic subunit of the yeast lysine acetyl-transferase NuA4 complex, acetylates the nuclear basket component Nup60 to promote mRNA export. Acetylat...
Preprint
Full-text available
Environmental oxidative stress threatens cellular integrity and should therefore be avoided by living organisms. Yet, relatively little is known about environmental oxidative stress perception. Here, using microfluidics, we show that the tail phasmid PHA neurons function as oxidative stress sensing neurons in C. elegans , and act in a complementary...
Article
Full-text available
The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient samples and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but causalities remain unclear. We used Saccharomyces cerevisiae to analyze how mitochondrial processes regulate the behavior of...
Preprint
Full-text available
The nuclear pore complex (NPC) mediates nearly all exchanges between nucleus and cytoplasm, and changes composition in many species as the organism ages. However, how these changes arise and whether they contribute themselves to aging is poorly understood. We show that in replicatively aging yeast cells attachment of DNA circles to NPCs drives the...
Preprint
Full-text available
In response to environmental stress, cellular defense strategies may be divided into two categories: those, as in homeostatic systems, that seek to maintain cell proliferation by degrading the stressor (i.e., resistance); and those that ensure cell survival (i.e. tolerance), even if this is often at the expense of cell proliferation. In this study,...
Preprint
Full-text available
The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient material and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but the causalities remained unclear. We used yeast as model system to analyze the relevance of mitochondrial processes for the...
Preprint
Full-text available
The life cycle of microorganisms is associated with dynamic metabolic transitions and complex cellular responses. In yeast, how metabolic signals control the progressive establishment of structural reorganizations observed in quiescent cells remains unclear. To address this question, we have developed a method that combines nutrient-limited prolife...
Article
Full-text available
Loss of proteostasis and cellular senescence are key hallmarks of aging, but direct cause-effect relationships are not well understood. We show that most yeast cells arrest in G1 before death with low nuclear levels of Cln3, a key G1 cyclin extremely sensitive to chaperone status. Chaperone availability is seriously compromised in aged cells, and t...
Article
Full-text available
A large number of genetic studies in yeast rely on the use of expression vectors. To facilitate the experimental approach of these studies, several collections of expression vectors have been generated (YXplac, pRS series, etc.). Subsequently, these collections have been expanded by adding more diversity to many of the plasmid features, including n...
Article
Full-text available
Budding yeast cells undergo a limited number of divisions before they enter senescence and die. Despite recent mechanistic advances, whether and how molecular events are temporally and causally linked during the transition to senescence remain elusive. Here, using real-time observation of the accumulation of extrachromosomal rDNA circles (ERCs) in...
Preprint
Full-text available
Loss of proteostasis and cellular senescence are key hallmarks of cell aging, but whether they are subject to direct cause-effect relationships is not known. We show that most yeast cells arrest in G1 before death with low nuclear levels of cyclin Cln3, a key activator of Start extremely sensitive to chaperone status. Chaperone availability is seri...
Article
Full-text available
Single-cell analysis commonly requires the confinement of cell suspensions in an analysis chamber or the precise positioning of single cells in small channels. Hydrodynamic flow focusing has been broadly utilized to achieve stream confinement in microchannels for such applications. As imaging flow cytometry gains popularity, the need for imaging-co...
Preprint
Full-text available
A large number of genetic studies in yeast rely on the use of expression vectors. To facilitate the experimental approach of these studies, several collections of expression vectors have been generated (YXplac, pRS series, etc.). Subsequently, these collections have been expanded by adding more diversity to many of the plasmid features, including n...
Article
Full-text available
In the above-mentioned article, the Supplemental movie files were inadvertently excluded. These files have now been added to the Supplemental Material online.
Article
Full-text available
In cells lacking telomerase, telomeres gradually shorten during each cell division to reach a critically short length, permanently activate the DNA damage checkpoint, and trigger replicative senescence. The increase in genome instability that occurs as a consequence may contribute to the early steps of tumorigenesis. However, because of the low fre...
Article
Full-text available
Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of hi...
Data
Mean duration of cell phases in specific mutant backgrounds.
Preprint
The accumulation of E xtrachromosomal r DNA C ircles (ERCs) and their asymmetric segregation upon division have been hypothesized to be responsible for replicative senescence in mother yeasts and rejuvenation in daughter cells. However, it remains unclear by which molecular mechanisms ERCs would trigger the irreversible cell cycle slow-down leading...
Preprint
Full-text available
Coordination of cell growth and division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established and maintained throughout the cell cycle remains to be discovered. Here, we developed a new...
Chapter
The generation of complex temporal stress patterns may be instrumental to investigate the adaptive properties of individual cells submitted to environmental stress on physiological timescale. However, it is difficult to accurately control stress concentration over time in bulk experiments. Here, we describe a microfluidics-based protocol to induce...
Book
The generation of complex temporal stress patterns may be instrumental to investigate the adaptive properties of individual cells submitted to environmental stress on physiological timescale. However, it is difficult to accurately control stress concentration over time in bulk experiments. Here, we describe a microfluidics-based protocol to induce...
Data
List of all strains used in this study. Table listing the strains used in this study as well as additional information about the genotypes and the origins of the strains. DOI: http://dx.doi.org/10.7554/eLife.23971.026
Article
Full-text available
Homeostatic systems that rely on genetic regulatory networks are intrinsically limited by the transcriptional response time, which may restrict a cell's ability to adapt to unanticipated environmental challenges. To bypass this limitation, cells have evolved mechanisms whereby exposure to mild stress increases their resistance to subsequent threats...
Article
Budding yeast cells have a finite replicative life span; that is, a mother cell produces only a limited number of daughter cells before it slows division and dies. Despite the gradual aging of the mother cell, all daughters are born rejuvenated and enjoy a full replicative lifespan. It has been proposed that entry of mother cells into senescence is...
Article
Primary cilia are necessary for shear stress sensing in different developing organs such as the kidneys and blood vessels. In endothelial cells (ECs), primary cilia bend in response to blood flow forces and are necessary for flow sensing as well as for the control of angiogenesis. The different parameters guiding cilia bending reflect the forces ge...
Article
Full-text available
In eukaryotes, telomeres cap chromosome ends to maintain genomic stability. Failure to maintain telomeres leads to their progressive erosion and eventually triggers replicative senescence, a pathway that protects against unrestricted cell proliferation. However, the mechanisms underlying the variability and dynamics of this pathway are still elusiv...
Article
In vertebrates, heart pumping is required for cardiac morphogenesis and altering myocardial contractility leads to abnormal intracardiac flow forces and valve defects [1-3]. Among the different mechanical cues generated in the developing heart, oscillatory flow has been proposed to be an essential factor in instructing endocardial cell fate toward...
Article
By implementing an external feedback loop one can tightly control the expression of a gene over many cell generations with quantitative accuracy. Controlling precisely the level of a protein of interest will be useful to probe quantitatively the dynamical properties of cellular processes and to drive complex, synthetically-engineered networks. In t...
Article
Cdc42 is a highly conserved master regulator of cell polarity. Here, we investigated the mechanism by which yeast cells never re-establish polarity at cortical sites (cytokinesis remnants [CRMs]) that have previously supported Cdc42-mediated growth as a paradigm to mechanistically understand how Cdc42-inhibitory polarity cues are established. We re...
Article
Full-text available
Video abstract: The pattern of blood flow has long been thought to play a significant role in vascular morphogenesis, yet the flow-sensing mechanism that is involved at early embryonic stages, when flow forces are low, remains unclear. It has been proposed that endothelial cells use primary cilia to sense flow, but this has never been tested in vi...
Article
Full-text available
In budding yeast, a mother cell can produce a finite number of daughter cells before it stops dividing and dies. Such entry into senescence is thought to result from a progressive decline in physiological function, including a loss of mitochondrial membrane potential (ΔΨ). Here, we developed a microfluidic device to monitor the dynamics of cell div...
Article
Full-text available
Pulsatile flow is a universal feature of the blood circulatory system in vertebrates and can lead to diseases when abnormal. In the embryo, blood flow forces stimulate vessel remodeling and stem cell proliferation. At these early stages, when vessels lack muscle cells, the heart is valveless and the Reynolds number (Re) is low, few details are avai...
Article
Full-text available
Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The kinetic proofreading (KPR) model pos...
Article
Full-text available
Gene expression plays a central role in the orchestration of cellular processes. The use of inducible promoters to change the expression level of a gene from its physiological level has significantly contributed to the understanding of the functioning of regulatory networks. However, from a quantitative point of view, their use is limited to short-...
Article
Type II topoisomerases are essential enzymes that modify DNA topology. These topoisomerases pass a double stranded segment (T-segment) of DNA though a transient double stranded break in a second segment (G-segment). This strand passage mechanism allows type II topoisomerases to unlink, unknot, and relax supercoiled DNA to below equilibrium levels1....
Article
In this issue, Trunnell et al. (2011) show that in mitotic entry the positive feedback that drives the activation of cyclin-dependent kinase (Cdk) involves a very ultrasensitive step of phosphorylation of Cdc25C by Cdk, thus strongly contributing to the switch-like behavior of this essential cell-cycle transition.
Article
During the past 10 years, major developments in live-cell imaging methods have accompanied growing interest in the application of microfluidic techniques to biological imaging. The broad design possibilities of microfabrication and its relative ease of implementation have led to the development of a number of powerful imaging assays. Specifically,...
Article
Full-text available
Silicon-based microscales allow real-time measurements of the growth rate of single cells and open up interesting perspectives for the study of mass biogenesis at the cellular level.
Article
Many promoters in eukaryotes have nucleosome-depleted regions (NDRs) containing transcription factor binding sites. However, the functional significance of NDRs is not well understood. Here, we examine NDR function in two cell cycle-regulated promoters, CLN2pr and HOpr, by varying nucleosomal coverage of the binding sites of their activator, Swi4/S...
Data
A model for phase-locking of an independent growth polarity oscillator by Clb2-CDK activity. A Schematic of coupled Clb-CDK and polarization oscillators. Clb-CDK can force the polarization oscillator during its sensitive period (shown here in red) to phase-lock the two oscillators. Pol., polarized growth; Depol., depolarized growth. B Left: uncoupl...
Data
Amplitude of bistability and probability of Start autoactivation as a function of model parameters. (A) Amplitude A of the bistability region as a function of n and k, calculated numerically using the deterministic model described by Equation 2. (B) Probability of observing feedback autoactivation (within 10 units of time) as a function of l and av...
Data
List of strains and plasmids. (0.02 MB DOC)
Data
Correlation of expression of MET3-driven fluorophores Venus and Cherry. (A) Top panel: time series of images (overlay of phase plus fluorescence) of a cell colony following a 20-min pulse of −Met. Cells carry MET3-Venus (false colored in green) and MET3-mCherry (colored in red). Bottom panel: phase images as in top panel, plus contours of scored ce...
Data
Comparison of cell proliferation in a standard 2% agar setup versus the microfluidic sandwich setup. Cells carrying a copy of CDC10-YFP were grown in the microfluidic device for 12 hours in SCD. Timelapse of cell growth using the standard agar method was carried out as previously described[7]. On the left is shown a sketch of the respective setups....
Data
Reversible Start transition in the absence of CLN1,2 feedback. cln1 cln2 cln3 GAL1pr-SIC1-4A MET3pr-CLN2 cells are shown following two consecutives 15-min-long pulses of exogenous CLN2 (at t = 540 min and t = 690 min). The three panels show phase contrast images, CLN2pr-Venus-degron signals, and Whi5-GFP signals, respectively. White lines indicate...
Data
Detection of nuclear fluorescence. (A) Fluorescence images showing the Whi5-GFP in WT cycling cells at indicated timings. The dark blue line indicates the cell contour (retrieved from phase contrast images). The cyan circle shows the position of the nucleus as determined by scoring Whi5-GFP using a custom procedure shown in Text S1. The white recta...
Data
Start activation of cln1 cln2 cln3 cells in response to a 5-min-long pulse of exogenous CLN2 (corresponding to the data described in Figure 2). The left panel shows phase contrast images. Cell contours are highlighted using different colors, depending on the response of each to the pulse: released cells (blue), G1 blocked cells (red), transiently a...
Data
Irreversible Start transition in the presence of CLN1,2 feedback. cln3 bck2 GAL1pr-SIC1-4A MET3pr-CLN2 cells are shown following a pulse of exogenous CLN2. Same legend as Video S3. The 15-min-long pulse is started at t = 540 min. (5.07 MB AVI)