Group leader: François Rouyer

Molecular Genetics of Circadian Rhythms

In brief

Our research aims at understanding how the brain controls sleep-wake rhythms. Sleep-wake rhythms are controlled by a brain circadian clock that is synchronized with day-night cycles by environmental cues, such as light and temperature. We use neurogenetics approaches in Drosophila to understand how a multi-oscillators brain clock is organized at the molecular and cellular levels as well as at the scale of neuronal networks, how the brain translates circadian information into sleep-wake rhythms, and how sensory signals are integrated to entrain the clock neuronal network and adapt the behavior to the environment.

Our projects address the following questions.

  • How does the molecular machinery that is running in the clock cells generate a 24h (circadian) oscillation: we analyze the function and regulation (transcriptional, post-transcriptional and post-translational controls) of key clock genes (Clock, period, timeless) and search for new clock components.
  • How natural genetic variation shapes individual sleep-wake rhythm phenotypes in various environmental conditions: we analyze the behavior of fully sequenced isogenic lines derived from individuals caught in the wild to identify new variants of clock and light-input components.
  • What is the neuronal basis of the brain circadian clock: we study the behavioral contribution of the different neuronal oscillators and their communication through neuropeptides (PDF and ITP) or other neurotransmitters to understand the rules operating in the clock neuronal network.
  • How do light changes synchronize the brain clock neuronal network with day-night cycles and modify its properties to adapt the behavior to the daily and seasonally changing environment: we characterize the neuronal and molecular pathways (photoreception through the visual system and cryptochrome) that transmit light signals to the clock neurons and their molecular oscillator.
  • How is the circadian information that is generated by the clock neurons translated into sleep-wake behavior: we search for clock neurons’ targets through anatomical and functional analysis and study sleep control features encoded by the clock neurons.
Teaching

Contribution to courses at Université Paris-Saclay, Master Life sciences and health:

  • Biologie du comportement animal (M1)
  • Atelier d’organismes modèles (M1)
  • Génétique du développement (M2)
  • Signalisation Cellulaire et Neurosciences (M2)

Other courses:

  • ENS Paris Saclay, Agrégation biologie (M1)
  • Université Pierre et Marie Curie, Master Écophysiologie (M2)

Hosting team for Masters’ internships (M1 and M2):

  • Université Paris-Saclay, Master Biologie-Santé
  • Université Paris-Diderot, Magistère Européen de Génétique
  • Université Pierre et Marie Curie, Masters « Biologie moléculaire et cellulaire » et « Biologie intégrative »
Grants
  • 2019-2023, F. Rouyer, PostClock : Posttranscriptional mechanisms in the Drosophila circadian clock, Agence Nationale de la Recherche (ANR), Programme blanc.
  • 2019-2022, F. Harms (coordinateur) and 3 associated laboratories, INOVAO: In-vivo neuroimaging using adaptive optics microscopy, Agence Nationale de la Recherche
  • 2018-2021, C. P. Kyriacou (coordinateur) and 10 european laboratories, CINCHRON: Comparative Insect Chronobiology, H2020 Marie Curie Inovative Training Network.
  • 2017-2020, K. Mouline (coordinatrice) and 3 associated laboratories, AnoRhythms: The Right Timing Makes the Good Vector (Daily Rhythms and how they Promote Adaptation to a Changing World in Major Malaria Vectors ), Agence Nationale de la Recherche (ANR), Programme blanc.
  • 2017-1019, F. Rouyer, Equipe FRM: Cellular and molecular mechanisms involved in the synchronization of sleep- wake cycles by the visual system, Fondation pour la Recherche Médicale.
  • 2017-2018, B. Bathellier, G. Fortin, P. Vernier (coordinateurs), Brainscopes : Multiscale dissection of the structure and function of the nervous system through novel imaging techniques, IDEX Paris Saclay
  • 2015-2017, D. Vasiliauskas (coordinateur) and 2 associated laboratories, NaturalNeuro: Identification of the natural variants of the development and function of the Drosophila nervous system, LIDEX NeuroSaclay, Université Paris-Saclay
  • 2014-2017, F. Rouyer, ClockEye: Control of sleep wake cycles by the visual system in Drosophila, Agence Nationale de la Recherche (ANR), Programme blanc.
  • 2013-2018, J-S Joly (coordinateur) and 5 associated laboratories, TEFOR: Transgenesis for Functional studies in model organisms, Investissements d’avenir, appel d’offres Infrastructures Nationales en Biologie et Santé.
  • 2013-2016, C. P. Kyriacou (coordinateur) and 12 European laboratories, INsecTIME: Molecular genetic study of insect biological timing, European Community, FP7 Marie Curie Initial Training Network.
  • 2013-2015, F. Rouyer (coordinateur), J-R Martin, S. Rétaux, P. Vernier, DrosoFish: Analyse fonctionnelle, anatomique et comportementale d’ensemble neuronaux chez des modèles drosophile et poisson. DIM Cerveau et Pensée, région Ile-de-France.
  • 2012-2014, J-R Martin (coordinateur) and F. Rouyer, FlyBrainImaging: Functional imaging of spontaneous activity in the Drosophila brain Mushroom-Bodies and their circadian regulation, Agence Nationale de la Recherche (ANR), Programme blanc.

PhD – Associated Doctoral Schools at Université Paris-Saclay:

  • Signalisations et réseaux intégratifs en biologie (BioSigne)
  • Structure et dynamique des systèmes vivants (SDSV)

Others: the lab is affiliated to “École des Neurosciences de Paris île-de-France” (ENP).

PhD theses defended in the laboratory
  • Rossana Serpe (2018), Identification of clock neurons and downstream circuits that are involved in sleep control in Drosophila melanogaster. Université Paris-Saclay, ED BioSigne (dir. F. Rouyer)
  • Joydeep De (2018), Daily and Seasonal Cues Modulate the Configuration of the Circadian Clock Neural Network. Université Paris-Saclay, ED BioSigne (dir. F. Rouyer)
  • Faredin Alejevski (2018), Photoentrainment of the Drosophila circadian clock though visual system. Université Paris-Saclay, ED SDSV (dir. F. Rouyer)
  • Alexandra Saint-Charles (2014), Contribution des rhodopsines et des récepteurs à l’histamine dans la synchronisation de l’horloge circadienne par le système visuel chez Drosophila melanogaster. Université Paris Sud, ED BioSigne (dir. F. Rouyer)
  • Simonetta Andreazza (2013), Analysis of new genes controlling Drosophila melanogaster rest-activity rhythms. Université Paris Sud, ED GGC (dir. F. Rouyer)
  • Alexandre Dognon (2011), Contrôle de la stabilité de TIMELESS par un complexe ubiquitine ligase de type Culline-3 dans l’horloge circadienne de Drosophila melanogaster. Université Paris Sud, ED BioSigne (dir. B. Grima)
  • Angélique Lamaze (2010), Etude de l’horloge circadienne chez Drosophila melanogaster : Etude du gène ctrip dans l’horloge moléculaire et mise en évidence d’un nouvel oscillateur neuronal dans l’horloge. Université Paris Sud, ED GGC (dir. F. Rouyer)
  • Paola Cusumano (2008), Control of rest-activity rhythms by the morning and evening oscillators in Drosophila melanogaster. Université Paris Sud, ED GGC (dir. F. Rouyer)
  • Benjamin Richier (2008), Rôle des gènes clock et clockwork orange dans l’horloge circadienne chez Drosophila melanogaster. Université Paris Sud, ED GGC (dir. F. Rouyer)
  • Ruohan Xia (2008), Roles of protein kinase A and ubiquitin protease USP8 in the Drosophila circadian clock. Université Paris Sud, ED GGC (dir. F. Rouyer)
  • Marie Picot (2007), Le réseau neuronal de l’horloge circadienne dans le cerveau de la drosophile : organisation fonctionnelle et entraînement par la lumière et la température. Université Paris Sud, ED BioSigne (dir. A. Klarsfeld)
  • Sébastien Malpel (2002), Etude fonctionnelle et développementale des interactions entre le système visuel et l’horloge circadienne de Drosophila melanogaster. Université Paris Diderot, (dir. A. Klarsfeld)
  • Eric Blanchardon (2002), Etude fonctionnelle des neurones d’horloge et recherche de nouveaux gènes impliqués dans le contrôle des rythmes circadiens chez la Drosophile. Université Paris Sud (dir. F. Rouyer)

Selected publications

  • Grima, B., Papin, C., Martin, B., Chélot, E., Ponien, P., Jacquet, E., and Rouyer, F. (2019). PERIOD-controlled deadenylation of the timeless transcript in the Drosophila circadian clock. Proc Natl Acad Sci U S A 116, 5721-5726. DOI: 10.1073/pnas.1814418116
  • Alejevski, F., Saint-Charles, A., Michard-Vanhée, C., Martin, B., Galant, S., Vasiliauskas, D., and Rouyer, F. (2019). The HisCl1 histamine receptor acts in photoreceptors to synchronize Drosophila behavioral rhythms with light-dark cycles. Nat Commun 10, 252. DOI: 10.1038/s41467-018-08116-7
  • Szabó, Á., Papin, C., Cornu, D., Chélot, E., Lipinszki, Z., Udvardy, A., Redeker, V., Mayor, U., and Rouyer, F. (2018). Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 23, 2273-2282. DOI: 10.1016/j.celrep.2018.04.064
  • Chatterjee, A., Lamaze, A., De, J., Mena, W., Chélot, E., Martin, B., Hardin, P., Kadener, S., Emery, P., and Rouyer, F. (2018). Reconfiguration of a Multi-oscillator Network by Light in the Drosophila Circadian Clock. Curr Biol 28, 2007-2017. DOI: 10.1016/j.cub.2018.04.064
  • Saint-Charles, A., Michard-Vanhée, C., Alejevski, F., Chélot, E., Boivin, A., and Rouyer, F. (2016). Four of the six Drosophila rhodopsin-expressing photoreceptors can mediate circadian entrainment in low light. J Comp Neurol 524, 2828-2844. DOI: 10.1002/cne.23994
  • Andreazza, S., Bouleau, S., Martin, B., Lamouroux, A., Ponien, P., Papin, C., Chélot, E., Jacquet, E., and Rouyer, F. (2015). Daytime CLOCK Dephosphorylation Is Controlled by STRIPAK Complexes in Drosophila. Cell Rep 11, 1266-1279. DOI: 10.1016/j.celrep.2015.04.033

Fly Activity Analysis Suite for Mac OSX

FaasX 32 bits is no longer supported and it is replaced by Faas as a 64 bits application compatible with MacOS 10.14 (Mojave) and above.

(FaasX is still downloadable for previous MacOS versions. < 10.14) Faas is a MacOS (10.14 ->10.15 and above) 64-bits application that is closely related to BRP (Brandeis Rhythm Package, D.A. Wheeler) to process DAMSystem (Trikinetics) fly activity data and provides you a more convenient graphic interface.

It was developed by M. Boudinot at the Institut de Neurobiologie Alfred Fessard, CNRS, in the group Molecular Genetics of Circadian Rhythms of François Rouyer.

Faas is self sufficient and does not need any other software, but experiment description files that are needed by Faas can be more easily created using Microsoft Excel and the provided Experiment template.

Features
Faas allows to run batch analysis with tabulated text and graphical rendering on circadian activity collected by DAMSystem such as:

  • cartesian and double plot of daily activity (Actogram).
  • average activity at each time interval throughout an entrained circadian cycle (Eduction).
  • period analysis periodogram
  • Periodogram (Cycle_p)
  • Autocorrelogram (Autocorrelation)
  • MESA power spectrum (MESA)
  • phase analysis (Phase).

Faas installation kits:

The provided data set can be used to test your installation and gives you example of files that are needed to run Faas.

Contacts:
Michel Boudinot
François Rouyer

Peer-reviewed Articles

2020

• Rouyer, F., and Chatterjee, A. (2020). Circadian Clocks: Structural Plasticity on the Input Side. Curr Biol 30, R890-R893. (Pubmed)

2019

• Hubert A, Harms F, Juvénal R, Treimany P, Levecq X, Loriette V, Farkouh G, Rouyer F, Fragola A. (2019). Adaptive optics light-sheet microscopy based on direct wavefront sensing without any guide star. Opt Lett. 44(10): 2514-2517. (Pubmed)
• Grima, B., Papin, C., Martin, B., Chélot, E., Ponien, P., Jacquet, E., and Rouyer, F. (2019). PERIOD-controlled deadenylation of the timeless transcript in the Drosophila circadian clock. Proc Natl Acad Sci U S A 116, 5721-5726. (Pubmed)
• Alejevski, F., Saint-Charles, A., Michard-Vanhée, C., Martin, B., Galant, S., Vasiliauskas, D., and Rouyer, F. (2019). The HisCl1 histamine receptor acts in photoreceptors to synchronize Drosophila behavioral rhythms with light-dark cycles. Nat Commun 10, 252. (Pubmed)

2018

• Sherrard, R. M., Morellini, N., Jourdan, N., El-Esawi, M., Arthaut, L. D., Niessner, C., Rouyer, F., Klarsfeld, A., Doulazmi, M., Witczak, J., d’Harlingue, A., Mariani, J., Mclure, I., Martino, C. F., and Ahmad, M. (2018). Low-intensity electromagnetic fields induce human cryptochrome to modulate intracellular reactive oxygen species. PLoS Biol 16, e2006229. (Pubmed)
• Chatterjee, A., Lamaze, A., De, J., Mena, W., Chélot, E., Martin, B., Hardin, P., Kadener, S., Emery, P., and Rouyer, F. (2018). Reconfiguration of a Multi-oscillator Network by Light in the Drosophila Circadian Clock. Curr Biol 28, 2007-2017. (Pubmed)
• Szabó, Á., Papin, C., Cornu, D., Chélot, E., Lipinszki, Z., Udvardy, A., Redeker, V., Mayor, U., and Rouyer, F. (2018). Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 23, 2273-2282. (Pubmed)
• Arganda-Carreras, I., Manoliu, T., Mazuras, N., Schulze, F., Iglesias, J. E., Bühler, K., Jenett, A., Rouyer, F., and Andrey, P. (2018). A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain. Front Neuroinform 12, 13. (Pubmed)

2017

• Klarsfeld, A., Birman, S., and Rouyer, F. (2018). Nobel time for the circadian clock Nobel Prize in Medicine 2017: Jeffrey C. Hall, Michael Rosbash and Michael W. Young. Med Sci (Paris) 34, 480-484. (Pubmed)

2016

• Chatterjee, A., and Rouyer, F. (2016). Control of sleep-wake cycles in Drosophila. In A time for metabolism and hormones, Sassone-Corsi, P., and Y. Christen, Springer), pp. 71-78.(Pubmed)
• Saint-Charles, A., Michard-Vanhée, C., Alejevski, F., Chélot, E., Boivin, A., and Rouyer, F. (2016). Four of the six Drosophila Rhodopsin-expressing photoreceptors can mediate circadian entrainment in low light. J Comp Neurol 524, 2828-2844. (Pubmed)

2015

• Rouyer, F., and Chatterjee, A. (2015). Circadian clocks: A receptor for subtle temperature changes. Nature 527, 449-451. (Pubmed)
• Rouyer, F. (2015). Gènes d’horloge: de la drosophile à l’homme. Bull Acad Natl Med 199, 1115-1131. (Pubmed)
• Andreazza, S., Bouleau, S., Martin, B., Lamouroux, A., Ponien, P., Papin, C., Chélot, E., Jacquet, E., and Rouyer, F. (2015). Daytime CLOCK Dephosphorylation Is Controlled by STRIPAK Complexes in Drosophila. Cell Rep 11, 1266-1279. (Pubmed)

2013

• Szabo, A., Papin, C., Zorn, D., Ponien, P., Weber, F., Raabe, T., and Rouyer, F. (2013). The CK2 kinase stabilizes CLOCK and represses its activity in the Drosophila circadian oscillator. PLoS Biol 11, e1001645. (Pubmed)
• Rouyer, F. (2013). Circadian Timing. In Neurosciences. From Molecule to Behavior: a university textbook, Ed: Galizia, C. G. and P.-M. Lledo.(Springer Spektrum), pp. 609-628.

2012

• Grima, B., Dognon, A., Lamouroux, A., Chelot, E., and Rouyer, F. (2012). CULLIN-3 Controls TIMELESS Oscillations in the Drosophila Circadian Clock. PLoS Biol 10, e1001367. (Pubmed)
• Rouyer, F. (2012). Circadian rhythms: No lazing on sunny afternoons. Nature 484, 325-326. (Pubmed
• Vieira, J., Jones, A. R., Danon, A., Sakuma, M., Hoang, N., Robles, D., Tait, S., Heyes, D. J., Picot, M., Yoshii, T., Helfrich-Forster, C., Soubigou, G., Coppee, J. Y., Klarsfeld, A., Rouyer, F., Scrutton, N. S., and Ahmad, M. (2012). Human cryptochrome-1 confers light independent biological activity in transgenic Drosophila correlated with flavin radical stability. PLoS One 7, e31867. (Pubmed)

2011

• Klarsfeld, A., Picot, M., Vias, C., Chelot, E., and Rouyer, F. (2011). Identifying specific light inputs for each subgroup of brain clock neurons in Drosophila larvae. J Neurosci 31, 17406-17415. (Pubmed)
• Lamaze, A., Lamouroux, A., Vias, C., Hung, H. C., Weber, F., and Rouyer, F. (2011). The E3 ubiquitin ligase CTRIP controls CLOCK levels and PERIOD oscillations in Drosophila. EMBO Rep 12, 549-557. (Pubmed)
• Rouyer, F. (2011). Les insectes, horloges modèles. Biofutur 30, 28-30.

2009

• Cusumano, P., Klarsfeld, A., Chélot, E., Picot, M., Richier, B., and Rouyer, F. (2009). PDF-modulated visual inputs and Cryptochrome define diurnal behavior in Drosophila. Nat Neurosci 12, 1427-1433. (Pubmed)
• Johard, H. A., Yoishii, T., Dircksen, H., Cusumano, P., Rouyer, F., Helfrich-Forster, C., and Nassel, D. R.(2009). Peptidergic clock neurons in Drosophila: Ion transport peptide and short neuropeptide F in subsets of dorsal and ventral lateral neurons. J Comp Neurol 516, 59-73. (Pubmed)
• Rieger, D., Wulbeck, C., Rouyer, F., and Helfrich-Forster, C. (2009). Period gene expression in four PDF-negative Lateral Neurons is sufficient for rhythmic activity of Drosophila melanogaster under dim light conditions. J Biol Rhythms 24, 271-282. (Pubmed)
• Picot, M., Klarsfeld, A., Chélot, E., Malpel, S., and Rouyer, F. (2009). A role for blind DN2 clock neurons in temperature entrainment of the Drosophila larval brain. J Neurosci 29, 8312-8320. (Pubmed)

2008

• Rouyer, F. (2008). Physiology: Mutant flies lack magnetic sense. Nature 454, 949-951. (Pubmed)
• Richier, B., Michard-Vanhée, C., Lamouroux, A., Papin, C., and Rouyer, F. (2008). The Clockwork Orange Drosophila Protein Functions as Both an Activator and a Repressor of Clock Gene Expression. J Biol Rhythms 23, 103-116. (Pubmed)

2007

• Picot, M., Cusumano, P., Klarsfeld, A., Ueda, R., and Rouyer, F. (2007). Light activates output from evening neurons and inhibits output from morning neurons in the Drosophila circadian clock. PLoS Biol 5, e315. (Pubmed)
• Helfrich-Forster, C., Yoshii, T., Wülbeck, C., Grieshaber, E., Rieger, D., Bachleitner, W., Cusumano, P., and Rouyer, F. (2007). The Lateral and Dorsal Neurons of Drosophila melanogaster: New insights about their morphology and function. Cold Spring Harb Symp Quant Biol 72, 517-525. (Pubmed)

2005

• Rouyer, F. (2005). Des horloges du matin et du soir dans le cerveau de la drosophile. Med Sci (Paris) 21, 808-810. (Pubmed)

2004

• Grima, B., Chélot, E., Xia, R., and Rouyer, F. (2004). Morning and evening peaks of activity rely on different clock neurons of the Drosophila brain. Nature 431, 869-873. (Pubmed)
• Klarsfeld, A., Malpel, S., Michard-Vanhée, C., Picot, M., Chélot, E., and Rouyer, F. (2004). Novel features of cryptochrome-mediated photoreception in the brain circadian clock of Drosophila. J Neurosci 24, 1468-1477. (Pubmed)
• Malpel, S., Klarsfeld, A., and Rouyer, F. (2004). Circadian synchronization and rhythmicity in larval photoperception-defective mutants of Drosophila. J Biol Rhythms 19, 10)-21. (Pubmed)

2003

• Klarsfeld, A., Leloup, J. C., and Rouyer, F. (2003). Circadian rhythms of locomotor activity in Drosophila. Behav Processes 64, 161-175. (Pubmed)

2002

• Grima, B., Lamouroux, A., Chélot, E., Papin, C., Limbourg-Bouchon, B., and Rouyer, F. (2002). The F-box protein SLIMB controls the levels of clock proteins PERIOD and TIMELESS. Nature 429, 178-182. (Pubmed)
• Malpel, S., Klarsfeld, A., and Rouyer, F. (2002). Larval optic nerve and adult extra-retinal photoreceptors sequentially associate with the clock neurons during Drosophila brain development. Development 129, 1443-1453. (Pubmed)

2001

• Blanchardon, E., Grima, B., Klarsfeld, A., Chélot, E., Hardin, P. E., Préat, T., and Rouyer, F. (2001). Defining the role of Drosophila lateral neurons in the control of circadian activity and eclosion rhythms by targeted genetic ablation and PERIOD protein overexpression. Eur J Neurosci 13, 871-888. (Pubmed)

1998

• Rouyer, F. (1998). Chez la drosophile, les horloges circadiennes ont leur propres yeux. Med Sci (Paris) 14, 448-450.
• Klarsfeld, A., and Rouyer, F. (1998). Effects of circadian mutations and LD periodicity on the life span of Drosophila melanogaster. J Biol Rhythms 13, 471-478. (Pubmed)

1997

• Rachidi, M., Lopes, C., Benichou, J.-C., and Rouyer, F. (1997). Analysis of period circadian expression in the Drosophila head by in situ hybridization. J Neurogenet 11, 255-263. (Pubmed)