DOCSLIB.ORG

Machine Learning Helps Identify CHRONO As a Circadian Clock Component

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Machine Learning Helps Identify CHRONO As a Circadian Clock Component Machine Learning Helps Identify CHRONO as a Circadian Clock Component Ron C. Anafi1,2.*, Yool Lee3., Trey K. Sato3., Anand Venkataraman3, Chidambaram Ramanathan4, Ibrahim H. Kavakli5, Michael E. Hughes6, Julie E. Baggs7, Jacqueline Growe1,2, Andrew C. Liu4, Junhyong Kim8, John B. Hogenesch2,3* 1 Division of Sleep Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America, 2 Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America, 3 Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America, 4 Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America, 5 Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey, 6 Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, United States of America, 7 Department of Pharmacology, Morehouse School of Medicine, Atlanta, Georgia, United States of America, 8 Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America Abstract Over the last decades, researchers have characterized a set of ‘‘clock genes’’ that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experi- mental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics. Citation: Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, et al. (2014) Machine Learning Helps Identify CHRONO as a Circadian Clock Component. PLoS Biol 12(4): e1001840. doi:10.1371/journal.pbio.1001840 Academic Editor: Ueli Schibler, University of Geneva, Switzerland Received August 27, 2013; Accepted March 7, 2014; Published April 15, 2014 Copyright: ß 2014 Anafi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work is supported by the National Institute of Neurological Disorders and Stroke (1R01NS054794-06 to ACL and JBH), the Defense Advanced Research Projects Agency (DARPA-D12AP00025 to John Harer, Duke University), an American Sleep Medicine Foundation Grant to RCA, and support from the National Institute on Aging (2P01AG017628-11) and the National Heart, Lung, and Blood Institute (5K12HL090021-05). This project is also funded, in part, by the Penn Genome Frontiers Institute under a HRFF grant with the Pennsylvania Department of Health, which disclaims responsibility for any analyses, interpretations or conclusions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Abbreviations: BIFC, bi-molecular fluorescence complementation; Chrono, computationally highlighted repressor of the network oscillator; co-IP, co- immunoprecipitation; D:D, constant darkness; ECDF, empirical cumulative distribution function; FDR, false discovery rate; GFP, green florescent protein; H3–K9, histone H3 lysine 9; HEK 293T, Human Embryonic Kidney 293 cells containing the SV40 T-Antigen; IF, immunofluorescence; L:D, light:dark; NIH 3T3, immortalized mouse fibroblast cell line; NS, nonspecific; PML, promyelocytic leukemia; qPCR, quantitative PCR; SCN, suprachiasmatic nuclei; U2OS, human osteosarcoma cell line; YFP, yellow florescent protein; ZT, zeitgeber time. * E-mail: [email protected] (RCA); [email protected] (JBH) . These authors contributed equally to this work. Introduction Period and Cryptochrome gene families are prominent among these targets, and their products ultimately repress CLOCK/ Circadian rhythms are ubiquitous in daily life, coordinating the BMAL1 activity and their own transcription [4,5]. A second loop sleep–wake cycle along with oscillations in hormone secretion, regulates Bmal1 expression through the opposing actions of the blood pressure, and cognitive function [1,2]. While a central REV–ERB and ROR nuclear receptor protein families [6,7]. master-pacemaker is located in the suprachiasmatic nuclei (SCN) Circadian oscillations are in turn subject to multiple layers of of the hypothalamus, cell autonomous rhythms are generated control. The casein kinase I proteins (CSNK1D and CSNK1E) throughout the body. The CLOCK/BMAL1 transcriptional and the F-box and leucine-rich repeat proteins (FBXL3, FBXL21) complex lies at the core of the molecular clock. These proteins [8–10] regulate the nuclear accumulation and/or stability of clock bind E-box elements in the promoters of target genes [3]. The components, respectively. Moreover, recent evidence highlights PLOS Biology | www.plosbiology.org 1 April 2014 | Volume 12 | Issue 4 | e1001840 Machine Learning Helps Identify A New Clock Component Author Summary Results and Discussion Daily rhythms are ever-present in the living world, driving In order to identify novel ‘‘core clock genes,’’ we considered the sleep–wake cycle and many other physiological changes. physiologically relevant features that define core circadian com- In the last two decades, several labs have identified ‘‘clock ponents: (1) Core clock components cycle with a ,24-h period. (2) genes’’ that interact to generate underlying molecular Core clock gene mutation or knockdown affects circadian behav- oscillations. However, many aspects of circadian molecular ioral rhythms. (3) Core clock genes interact with other core clock physiology remain unexplained. Here, we used a simple genes. (4) Core clock genes are expressed in most tissues. (5) Core ‘‘machine learning’’ approach to identify new clock genes clock genes are phylogenically conserved between vertebrates and by searching the genome for candidate genes that share flies. clock-like features such as cycling, broad-based tissue RNA Importantly, as is demonstrated by our exemplar set of known expression, in vitro circadian activity, genetic interactions, clock genes (Figure 1A), none of these features are absolute require- and homology across species. Genes were ranked by their ments: The canonical circadian gene Clock, for example, does not similarity to known clock components and the candidates cycle robustly in the pituitary [25] or SCN [26]. Individual knock- were screened and validated for evidence of clock func- down of either the Nr1d1 or Nr1d2 genes has minimal phenotypic tion in vitro. One candidate, which we renamed CHRONO effect [27]. Rather, these features lie on a continuum, each lending (Gm129), interacted with the master regulator of the clock, BMAL1, disrupting its transcriptional activity. We found that some support to a given gene having a core circadian function. Chrono knockout mice had prolonged locomotor activity We used published, genome-wide datasets that provide infor- rhythms, getting up progressively later each day. Our mation on each of these features and developed simple, albeit experiments demonstrated that CHRONO interferes with imperfect, metrics to quantify each feature. These metrics were the ability of BMAL1 to recruit CBP, a bona fide histone designed to reward clock-like features. acetylase and key transcriptional coactivator of the circa- dian clock. Core Clock Metrics Cycling. In order to assess transcript cycling, we reanalyzed high-resolution time course microarray data for liver, pituitary, the importance of metabolic cofactors and histone modifiers (e.g., and NIH 3T3 cells [25]. As detailed in the Materials and Methods HDAC3, P300, CBP, SIRT1, and NAMPT) in modulating these section, we combined the p values obtained by evaluating cycling feedback loops. in each tissue to create a single general cycling metric (MCyc) for The understanding of circadian timekeeping has demonstrated each gene. Higher values of MCyc correspond
Load more

Recommended publications
  • The Ins and Outs of Circadian Timekeeping Steven a Brown* and Ueli Schibler†
    gd9507.qxd 11/10/1999 12:14 PM Page 588 588 The ins and outs of circadian timekeeping Steven A Brown* and Ueli Schibler† Recent research in Drosophila and in mammals has generated The mechanism by which light signals entrain the clock is fascinating new models for how circadian clocks in these another topic of intense interest, and will be our other focus. organisms are reset by light and how these clocks, in turn, direct circadian outputs. Though light perception by the central clock is Central clock mechanisms: a brief summary ocular in mammals, it probably proceeds via a mechanism In all cases examined to date, circadian clocks have been separate from traditional visual transduction. In Drosophila, one cell-autonomous: a single cell can generate and maintain mechanism is non-ocular and is in fact present in many different self-sustained circadian oscillations. The molecular basis tissues. In both organisms, the cryptochrome family of for these rhythms may rely on a negative feedback loop in photoreceptor-like molecules plays a role in the circadian clock, which clock proteins negatively regulate their own abun- though their function is incompletely understood. Moreover, dance or activity. This regulation may occur both at the although a master clock resides in the brain, a functional clock transcriptional and at the post-transcriptional level. For appears to reside in most cells of the body. In these tissues, at example, in the bread mold Neurospora crassa, the Fre- least some output genes are controlled at the transcriptional quency protein negatively regulates its own transcription level directly by clock proteins; others appear to be regulated by by interfering with the ability of the White-collar-1 and cascades of circadian transcription factors.
    [Show full text]
  • 2009 Riboclub Program
    RiboClub 2017 in association with the Swiss National Center of Competence in RNA & Disease. September 24-28 RNPs: the Good, the Bad and the Ugly Insights into RNA-protein complex assembly and function in health and disease Hotel et Villégiature Chéribourg 2603 Chemin du Parc Orford (Magog) Quebec, Canada Sunday, September 24th 15:00 – 18:00 Registration for early arrivals 18:00 – 19:30 Welcome reception 19:30 – 21:30 Opening dinner Monday, September 25th 08:00 – 08:45 Registration 08:45 – 08:55 Opening Notes and Announcements (Sherif Abou Elela) 08:55 – 09:10 Welcome Notes by Beat Nobs, Ph.D., Swiss Ambassador to Canada 09:10 – 09:15 Presentation of Keynote speaker (Oliver Mühlemann) 09:15 – 10:15 Keynote presentation From bench to clinical trial: microRNA 122 as an antiviral target for hepatitis C virus Peter Sarnow, Stanford University, Stanford 10:15 – 10:45 Coffee break Session 1: Non-coding RNA function Chair: Martin Jinek (Host: Benoit Chabot) 10:45 – 10:50 Introduction by Martin Jinek 10:50 – 11:05 Mbnl1-dependent mis-regulation and mis-splicing of a conserved myogenic lncRNA in myotonic dystrophy type 1 Pascal Chartrand, Universite de Montreal, Montreal 11:05 – 11:30 Non-canonical function of DGCR8 controls mESCs exit from pluripotency Constance Ciaudo, ETH Zurich, Zurich 11:30 – 11:45 microRNAs use different ways to regulate gene expression in animals Martin Simard, Universite Laval, Quebec 11:45 – 12:10 Structure, evolution and targeting of non coding RNAs Gabriele Varani, University of Washington, Seattle 12:10 – 12:35 Structural
    [Show full text]
  • The for Report 07-08
    THE CENTER FOR INTEGRATIVE GENOMICS REPORT 07-08 www.unil.ch/cig Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 RESEARCH 6 Richard Benton Chemosensory perception in Drosophila: from genes to behaviour 8 Béatrice Desvergne Networking activity of PPARs during development and in adult metabolic homeostasis 10 Christian Fankhauser The effects of light on plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 Nouria Hernandez Mechanisms of basal and regulated RNA polymerase II and III transcription of ncRNA in mammalian cells 16 Winship Herr Regulation of cell proliferation 18 Henrik Kaessmann Mammalian evolutionary genomics 20 Sophie Martin Molecular mechanisms of cell polarization 22 Liliane Michalik Transcriptional control of tissue repair and angiogenesis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and the sleep EEG 30 Bernard Thorens Molecular and physiological analysis of energy homeostasis in health and disease 32 Walter Wahli The multifaceted roles of PPARs 34 Other groups at the Génopode 37 CORE FACILITIES 40 Lausanne DNA Array Facility (DAFL) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD at the CIG 52 Seminars and symposia 54 The CIG annual retreat 62 The CIG and the public 63 Artist in residence at the CIG 63 PEOPLE 64 1 Introduction The Center for IntegratiVE Genomics (CIG) at A glance The Center for Integrative Genomics (CIG) is the newest depart- ment of the Faculty of Biology and Medicine of the University of Lausanne (UNIL).
    [Show full text]
  • Circadian Rhythms: Mop up the Clock !
    Article Circadian rhythms: Mop up the clock ! BROWN, Steven, SCHIBLER, Ulrich Abstract All circadian clock genes discovered in Drosophila have mammalian counterparts with extensive sequence homology. Similarities and differences have been identified between insect and mammalian oscillators. Recent studies have shed new light on two mammalian clock components: Mop3 and Per2. Reference BROWN, Steven, SCHIBLER, Ulrich. Circadian rhythms: Mop up the clock ! Current Biology, 2001, vol. 11, no. 7, p. R268-R270 DOI : 10.1016/S0960-9822(01)00135-X Available at: http://archive-ouverte.unige.ch/unige:123132 Disclaimer: layout of this document may differ from the published version. 1 / 1 R268 Dispatch Circadian rhythms: Mop up the clock! Steven A. Brown and Ueli Schibler All circadian clock genes discovered in Drosophila have cryptochrome (cry). The products of these clock genes can mammalian counterparts with extensive sequence be assembled into a negative feedback loop that provides homology. Similarities and differences have been a plausible molecular mechanism for rhythm generation identified between insect and mammalian oscillators. (for review, see [5]). Recent studies have shed new light on two mammalian clock components: Mop3 and Per2. In the proposed circuitry, Clk and Cyc — transcription factors with PAS-helix-loop-helix domains — activate the Address: Département de Biologie Moléculaire, Sciences II, Université de Genève 30, Quai Ernest Ansermet, CH-1211 Genève-4, transcription of the per and tim genes. Per and Tim proteins Switzerland. then block transcription of their own genes. As a conse- E-mail: [email protected]; [email protected] quence, Per and Tim levels decrease, and a new 24 hour wave of per and tim transcription can initiate.
    [Show full text]
  • EMBO Facts & Figures
    excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology.
    [Show full text]
  • Role of the Nuclear Receptor Rev-Erb Alpha in Circadian Food Anticipation and Metabolism Julien Delezie
    Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism Julien Delezie To cite this version: Julien Delezie. Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism. Neurobiology. Université de Strasbourg, 2012. English. NNT : 2012STRAJ018. tel- 00801656 HAL Id: tel-00801656 https://tel.archives-ouvertes.fr/tel-00801656 Submitted on 10 Apr 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE CNRS UPR 3212 · Institut des Neurosciences Cellulaires et Intégratives THÈSE présentée par : Julien DELEZIE soutenue le : 29 juin 2012 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Neurosciences Rôle du récepteur nucléaire Rev-erbα dans les mécanismes d’anticipation des repas et le métabolisme THÈSE dirigée par : M CHALLET Etienne Directeur de recherche, université de Strasbourg RAPPORTEURS : M PFRIEGER Frank Directeur de recherche, université de Strasbourg M KALSBEEK Andries
    [Show full text]
  • Cell Size Regulation, a Mechanism That Controls Cellular RNA Accumulation
    Cell Size Regulation, a Mechanism That Controls Cellular RNA Accumulation: Consequences on Regulation of the Ubiquitous Transcription Factors Oct1 and NF-Y, and the Liver-enriched Transcription Factor DBP Edward E. Schmidt and Ueli Schibler Department of Molecular Biology, University of Geneva, Sciences II, CH-1211 Geneva-4 Switzerland Abstract. Cell sizes can differ vastly between cell per protein DBP correlate closely to cellular Downloaded from http://rupress.org/jcb/article-pdf/128/4/467/1401380/467.pdf by guest on 24 September 2021 types in individual metazoan organisms. In rat liver, RNA:DNA ratios. Our results suggest that DBP spleen, and thymus, differences in average cell size mRNA levels, like rRNA levels, are transcriptionally roughly reflect differences in RNA:DNA ratios. For determined. Thus the dbp gene, like the ribosomal example, hepatocytes were found to have a cytoplas- genes, may be subject to cell size regulation. As a mic:nuclear volume ratio and an RNA:DNA ratio consequence, nuclei from liver, a tissue with a very which were 34- and 21-fold higher, respectively, than large average cell size, accumulated higher levels of those in thymocytes. RNA synthesis per DNA- DBP protein than nuclei from small-celled tissues, equivalent in the hepatocytes was 25-fold greater than such as spleen or lung. In contrast to DBP, the ubiq- that in thymocytes, suggesting that differences in over- uitous transcription factors Octl and NF-Y escaped all transcriptional activity, not differences in overall cell size control. Nuclei from most tissues contained RNA stability, were primarily responsible for deter- similar amounts of these factors irrespective of cell mining cellular RNA:DNA ratios.
    [Show full text]
  • JOSEF JIRICNY 15.40 Malcolm D
    PROGRAM 13.00 Walter Schaffner Institute of Molecular Life Sciences, University of Zurich Opening th 13.10 Walter J. Gehring 60 Birthday Growth & Development, Biocentre, University of Basel Symposium Master Control Genes and the Evolution of Vision 13.50 Iain Mattaj EMBL, Heidelberg Regulating Nuclear Dynamics 14.30 Coffee Break 15.00 Ueli Schibler Department of Molecular Biology, University of Geneva The Mammalian Circadian Timing System: a Clock in Every Cell JOSEF JIRICNY 15.40 Malcolm D. Walkinshaw Institute of Structural and Molecular Biology, University of Edinburgh The Glycolytic Pathway as a Target for Structure Based Inhibitor Design 16.20 Witold Filipowicz Friedrich Miescher Institute for Biomedical Research, Basel Friday, 29 April 2011 Regulation of miRNA Function and Metabolism in Mammalian Cells Auditorium Maximum, ETH Zurich 17.00 Short Break 17.10 Irene Bozzoni University of Rome, La Sapienza Role of miRNA Deregulation in Duchenne Muscular Dystrophy 17.50 Laurence H. Pearl Sussex Centre for Genome Damage and Stability, University of Sussex Knowing Me, Knowing U - Joe Jiricny and Base Excision 18.30 Closing Remarks 18.40 Apéro CONTACT: Institute of Molecular Cancer Research: [email protected] IRENE BOZZONI LAURENCE H. PEARL began his research career at Birkbeck College and started his own laboratory at studied biology at La Sapienza University of Rome and obtained her Ph.D. in University College London in 1989, becoming Professor of Structural Biology in 1975. After a post-doc at the Institute of Molecular Biology II of the University of 1996. He was Professor of Protein Crystallography at the Institute of Cancer Re- Zurich, she held various research positions at the Centro Acidi Nucleici of C.N.R.
    [Show full text]
  • Why the Rat-1 Fibroblast Minireview Should Replace the SCN As the in Vitro Model of Choice
    Cell, Vol. 93, 917±919, June 12, 1998, Copyright 1998 by Cell Press Why the Rat-1 Fibroblast Minireview Should Replace the SCN as the In Vitro Model of Choice Michael Rosbash Rhythm work in nonmammalian systems has flowered Howard Hughes Medical Institute of late but often within less elegant cell types than retinal NSF, Center for Biological Timing and SCN neurons. Photosynthetic bacteria and Neuro- Department of Biology spora house bona fide circadian rhythms (Dunlap, 1996), Brandeis University but the absence of a tight biochemical connection with Waltham, Massachusetts 02254 mammals (the same protein doing the same job) makes it understandable why these lower animal rhythms are (SCN: your daysÐand nightsÐare numbered) not prominently featured within the Society for Neurosci- ence. Drosophila circadian rhythms are less easy to dismiss, as they occur within neuronal as well as non- Every once in a while there appears a set of experiments neuronal cell types (Liu et al., 1988; Siwicki et al., 1988). that changes the way a field views itself. This is certainly Moreover, tight molecular connections between fruit fly the case with the Balsalobre et al. (1998) paper published and mammalian rhythms now exist, thanks in large part in this issue of Cell. The key results were presented to the discovery of mammalian period (mper) genes (Sun by Ueli Schibler at the recent Society for Research on et al., 1997; Tei et al., 1997). Remarkably, at least two Biological Rhythms Meeting in Amelia Island, Florida mper transcripts are expressed and undergo circadian (May 6±10), and there was an audible collective gasp in oscillations in level within the SCN.
    [Show full text]
  • 1 Supplemental Material and Methods for Circadian Hepatocyte Clocks
    Supplemental Material and Methods for Circadian hepatocyte clocks keep synchrony in the absence of a master pacemaker in the suprachiasmatic nucleus or other extrahepatic clocks Flore Sinturel, Pascal Gos, Volodymyr Petrenko, Claudia Hagedorn, Florian Kreppel, Kai- Florian Storch, Darko Knutti, Andre Liani, Charles Weitz, Yann Emmenegger, Paul Franken, Luigi Bonacina, Charna Dibner and Ueli Schibler Correspondence to: [email protected]; [email protected] Supplemental materials and methods Generation of “Hepatocyte clock-only mice” The generation of the Bmal1 stopped allele has been performed by modification of the targeting vector for the Bmal1 floxed allele (Storch et al. 2007). The LoxP-site flanked stop cassette was engineered to contain an engrailed 2-based splice acceptor (Mitchell et al. 2001) followed by d2EGFP (Clontech) in-frame, a triple repeat of a SV40 polyA signal and PGKβgeo. The latter represents a pgk-driven neo-β-galactosidase fusion gene that was FRT-flanked. The cassette was inserted into the single AvrII site inside the intron between Bmal1 exon 5 and 6 of the targeting vector. ES cell targeting and mouse blastocyst injections was carried out according to standard methods. Genotyping was performed using multiplex PCR and primers (Supplemental Table S2). RT-Biolumicorder system The RT-Biolumicorder (Lesa technology SA) has been designed and engineered as described in (Saini et al. 2013). It consists of a cylindrical cage equipped with a photomultiplier tube, highly light reflective walls, a programmable feeding machine, a water flask equipped with an ultrasonic device measuring water consumption, and an infrared sensor allowing the 1 simultaneous recording of locomotor activity.
    [Show full text]
  • The Circadian Symphony
    presents Science meets Music THE CIRCADIAN SYMPHONY Musical Performance by Hilda Huang Piano & Scientific Lecture by Dr. Ueli Schilber Friday, November 27th, 2020 19:00 Virtual Event Program Introduction Dr. Gabriella Lundkvist Musica Ricercata Nr. 1 György Ligeti (1923-2006) Hilda Huang ******************* Scientific Lecture "The Circadian Symphony: a 24-hour clock in every body cell" Prof. Dr. Ueli Schibler ******************* Toccata C Minor J. S. Bach (1685-1750) Fantasy op. 77 Ludwig van Beethoven (1770-1827) Hilda Huang ****************** Questions & Answers Hilda Huang, Prof. Schibler A very special thanks to Dan Hummel, Lars Klostermann, Joseph Patrych and the University of Geneva for helping us put the video together. Hilda Huang “Whoever says Hilda Huang must also say Bach.” (Leipzig Bach Archive) The pianist’s lifelong devotion to the music of Bach earned her the first prize at the Leipzig International Bach Competition at the age of 18, whereupon she began her international concert career on the Steinway and Sons Prizewinners’ Concert Network with debuts at the Leipzig Gewandhaus and Montreal Bach Festival. During this time, she earned her B.S. in Chemistry from Yale College, and a string of personal obstacles that challenged her ability to perform. Leaning on Bach’s music and the formative relationships she cultivated through her music studies, she recognized the motivations directing her musical trajectory, her performances on historical keyboards, and her study of pedagogy and theory. She began to teach at Yale College and the Yale School of music, working to empower students by resolving traditions of interpretation- performance through theoretical frameworks cultivated by systems and languages of pedagogy.
    [Show full text]
  • Systems Biology of Mammalian Circadian Clocks
    ANRV404-PH72-28 ARI 18 January 2010 10:16 Systems Biology of Mammalian Circadian Clocks Hideki Ukai1 and Hiroki R. Ueda1,2 1Laboratory for Systems Biology and 2Functional Genomics Unit, RIKEN Center for Developmental Biology, Hyogo 650-0047, Japan; email: [email protected] Annu. Rev. Physiol. 2010. 72:579–603 Key Words First published online as a Review in Advance on transcriptional circuit, temperature compensation, singularity, November 13, 2009 artificial circuit The Annual Review of Physiology is online at by University of Tokyo on 02/14/10. For personal use only. physiol.annualreviews.org Abstract This article’s doi: Systems biology is a natural extension of molecular biology; it can be 10.1146/annurev-physiol-073109-130051 defined as biology after identification of key gene(s). Systems-biological Copyright c 2010 by Annual Reviews. research is a multistage process beginning with (a) the comprehensive Annu. Rev. Physiol. 2010.72:579-603. Downloaded from arjournals.annualreviews.org ! All rights reserved identification and (b) quantitative analysis of individual system com- 0066-4278/10/0315-0579$20.00 ponents and their networked interactions, which lead to the ability to (c) control existing systems toward the desired state and (d ) design new ones based on an understanding of the underlying structure and dynam- ical principles. In this review, we use the mammalian circadian clock as a model system and describe the application of systems-biological ap- proaches to fundamental problems in this model. This application has allowed the identification of transcriptional/posttranscriptional circuits, the discovery of a temperature-insensitive period-determining process, and the discovery of desynchronization of individual clock cells under- lying the singularity behavior of mammalian clocks.
    [Show full text]