Circadian Rhythms and Biological Clocks Part A, PDF
Preview Circadian Rhythms and Biological Clocks Part A,
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON and MELVIN I. SIMON Division of Biology California Institute of Technology Pasadena, California ANNA MARIE PYLE Departments of Molecular, Cellular and Developmental Biology and Department of Chemistry Investigator Howard Hughes Medical Institute Yale University Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 225WymanStreet,Waltham,MA02451,USA 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 125LondonWall,LondonEC2Y5AS,UK TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UK Firstedition2015 Copyright©2015ElsevierInc.Allrightsreserved. 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ISBN:978-0-12-801218-5 ISSN:0076-6879 ForinformationonallAcademicPresspublications visitourwebsiteatstore.elsevier.com CONTRIBUTORS KatharineAbruzzi DepartmentofBiology,HowardHughesMedicalInstituteandNationalCenterfor BehavioralGenomics,BrandeisUniversity,Waltham,Massachusetts,USA J.DouglasArmstrong ActualAnalytics,Edinburgh,UnitedKingdom SofiaAxelrod LaboratoryofGenetics,TheRockefellerUniversity,NewYork,USA JasperBosman DepartmentofMolecularChronobiology,Groningen,TheNetherlands JosephS.Boyd CenterforCircadianBiology,UniversityofCalifornia,SanDiego,LaJolla,California,USA JoonseokCha DepartmentofPhysiology,UniversityofTexasSouthwesternMedicalCenter,Dallas,TX, USA XiaoChen DepartmentofBiology,HowardHughesMedicalInstituteandNationalCenterfor BehavioralGenomics,BrandeisUniversity,Waltham,Massachusetts,USA SusanE.Cohen CenterforCircadianBiology,andDivisionofBiologicalSciences,UniversityofCalifornia, SanDiego,LaJolla,California,USA RodolfoCosta DepartmentofBiology,UniversityofPadova,Padova,Italy JayC.Dunlap DepartmentofGenetics,GeiselSchoolofMedicineatDartmouth,Hanover,New Hampshire,USA HaoA.Duong DepartmentofNeurobiology,HarvardMedicalSchool,Boston,Massachusetts,USA ZhengEelderink-Chen DepartmentofMolecularChronobiology,Groningen,TheNetherlands MartinEgli DepartmentofBiochemistry,SchoolofMedicine,VanderbiltUniversity,Nashville, Tennessee,USA MarcellaL.Erb DivisionofBiologicalSciences,UniversityofCalifornia,SanDiego,LaJolla,California, USA xi xii Contributors JavierEspinosa DivisionofGenetics,UniversityofAlicante,Alicante,Spain Jin-YuanFan DivisionofMolecularBiologyandBiochemistry,SchoolofBiologicalSciences,University ofMissouri-KansasCity,KansasCity,Missouri,USA MichaelGebert DepartmentofNeurobiology,HarvardMedicalSchool,Boston,Massachusetts,USA SusanS.Golden CenterforCircadianBiology,andDivisionofBiologicalSciences,UniversityofCalifornia, SanDiego,LaJolla,California,USA GregoryR.Grant DepartmentofGenetics,UniversityofPennsylvania,Philadelphia,Pennsylvania,USA,and PennCenterforBioinformatics,UniversityofPennsylvania,Philadelphia,Pennsylvania, USA CarlaB.Green DepartmentofNeuroscience,UniversityofTexasSouthwesternMedicalCenter,Dallas, Texas,USA EdwardW.Green DepartmentofGenetics,UniversityofLeicester,Leicester,UnitedKingdom RalphJ.Greenspan CenterforCircadianBiology,andKavliInstituteforBrainandMind,Universityof California,SanDiego,California,USA PaulE.Hardin DepartmentofBiologyandCenterforBiologicalClocksResearch,TexasA&MUniversity, CollegeStation,Texas,USA MatthewM.Hindle SynthSysandSchoolofBiologicalSciences,UniversityofEdinburgh,Edinburgh,United Kingdom TsuyoshiHirota MolecularandComputationalBiologySection,UniversityofSouthernCalifornia,Los Angeles,California,USA,andInstituteofTransformativeBio-Molecules,Nagoya University,Nagoya,Japan JohnB.Hogenesch DepartmentofPharmacology,InstituteforTranslationalMedicineandTherapeutics, UniversityofPennsylvaniaSchoolofMedicine,Philadelphia,Pennsylvania,USA Hung-ChungHuang DepartmentofNeuroscience,UniversityofTexasSouthwesternMedicalCenter,Dallas, Texas,USA MichaelE.Hughes DepartmentofBiology,UniversityofMissouri-St.Louis,St.Louis,Missouri,USA Contributors xiii JenniferHurley DepartmentofGenetics,GeiselSchoolofMedicineatDartmouth,Hanover,New Hampshire,USA TakeoKatsuki KavliInstituteforBrainandMind,UniversityofCalifornia,SanDiego,California,USA SteveA.Kay MolecularandComputationalBiologySection,UniversityofSouthernCalifornia, LosAngeles,California,USA,andInstituteofTransformativeBio-Molecules,Nagoya University,Nagoya,Japan AndrewKeightley DivisionofMolecularBiologyandBiochemistry,SchoolofBiologicalSciences,University ofMissouri-KansasCity,KansasCity,Missouri,USA JinYoungKim DepartmentofNeurobiology,HarvardMedicalSchool,Boston,Massachusetts,USA Tae-KyungKim DepartmentofNeuroscience,UniversityofTexasSouthwesternMedicalCenter,Dallas, Texas,USA Yong-IckKim CenterforCircadianBiology,UniversityofCalifornia,SanDiego,LaJolla,California,USA NobuyaKoike DepartmentofNeuroscience,UniversityofTexasSouthwesternMedicalCenter,Dallas, Texas,USA ShihokoKojima DepartmentofBiologicalSciences,VirginiaTech,Blacksburg,VA,USA JohannaKrahmer SynthSysandSchoolofBiologicalSciences,UniversityofEdinburgh,Edinburgh,United Kingdom VivekKumar DepartmentofNeuroscience,andHowardHughesMedicalInstitute,UniversityofTexas SouthwesternMedicalCenter,Dallas,Texas,USA PieterBasKwak DepartmentofNeurobiology,HarvardMedicalSchool,Boston,Massachusetts,USA CharalambosP.Kyriacou DepartmentofGenetics,UniversityofLeicester,Leicester,UnitedKingdom ThierryLeBihan SynthSysandSchoolofBiologicalSciences,UniversityofEdinburgh,Edinburgh,United Kingdom TanyaL.Leise DepartmentofMathematicsandStatistics,AmherstCollege,Amherst,Massachusetts,USA JiajiaLi DepartmentofBiology,UniversityofMissouri-St.Louis,St.Louis,Missouri,USA xiv Contributors YiLiu DepartmentofPhysiology,UniversityofTexasSouthwesternMedicalCenter,Dallas,TX, USA JenniferJ.Loros DepartmentofGenetics,GeiselSchoolofMedicineatDartmouth,Hanover,New Hampshire,USA,andDepartmentofBiochemistry,GeiselSchoolofMedicineat Dartmouth,Hanover,NewHampshire,USA SarahF.Martin SynthSysandSchoolofBiologicalSciences,UniversityofEdinburgh,Edinburgh,United Kingdom JohnC.Means DivisionofMolecularBiologyandBiochemistry,SchoolofBiologicalSciences,University ofMissouri-KansasCity,KansasCity,Missouri,USA MarthaMerrow DepartmentofMolecularChronobiology,Groningen,TheNetherlands,andInstituteof MedicalPsychology,Munich,Germany AndrewJ.Millar SynthSysandSchoolofBiologicalSciences,UniversityofEdinburgh,Edinburgh,United Kingdom EmiNagoshi DepartmentofGeneticsandEvolution,UniversityofGeneva,Geneva,Switzerland PrachiNakashe DepartmentofNeuroscience,UniversityofTexasSouthwesternMedicalCenter,Dallas, Texas,USA EmmaK.O’Callaghan ActualAnalytics,Edinburgh,UnitedKingdom MariaOlmedo InstituteofMedicalPsychology,Munich,Germany MarkL.Paddock CenterforCircadianBiology,UniversityofCalifornia,SanDiego,California,USA MirkoPegoraro DepartmentofGenetics,UniversityofLeicester,Leicester,UnitedKingdom JoePogliano DivisionofBiologicalSciences,UniversityofCalifornia,SanDiego,LaJolla,California, USA JeffreyL.Price DivisionofMolecularBiologyandBiochemistry,SchoolofBiologicalSciences,University ofMissouri-KansasCity,KansasCity,Missouri,USA Contributors xv MichaelRosbash DepartmentofBiology,HowardHughesMedicalInstituteandNationalCenterfor BehavioralGenomics,BrandeisUniversity,Waltham,Massachusetts,USA LinoSaez LaboratoryofGenetics,TheRockefellerUniversity,NewYork,USA RyanK.Shultzaberger CenterforCircadianBiology,andKavliInstituteforBrainandMind,Universityof California,SanDiego,California,USA JosephS.Takahashi DepartmentofNeuroscience,andHowardHughesMedicalInstitute,UniversityofTexas SouthwesternMedicalCenter,Dallas,Texas,USA CharlesJ.Weitz DepartmentofNeurobiology,HarvardMedicalSchool,Boston,Massachusetts,USA MichaelW.Young LaboratoryofGenetics,TheRockefellerUniversity,NewYork,USA WangjieYu DepartmentofBiologyandCenterforBiologicalClocksResearch,TexasA&MUniversity, CollegeStation,Texas,USA AbbyZadina DepartmentofBiology,HowardHughesMedicalInstituteandNationalCenterfor BehavioralGenomics,BrandeisUniversity,Waltham,Massachusetts,USA JianZhou DepartmentofBiologyandCenterforBiologicalClocksResearch,TexasA&MUniversity, CollegeStation,Texas,USA MianZhou DepartmentofPhysiology,UniversityofTexasSouthwesternMedicalCenter,Dallas,TX, USA PREFACE Inthe10yearssinceapreviouscircadianvolumeofMethodsinEnzymology waspublished,thecircadianfieldhasevolvedwiththeintroductionofnew concepts, new approaches, and, of course, many new investigators. As the previousvolumewasprecededbyanexplosionofdiscoveriesandinforma- tion about how clocks work in diverse organisms, from cyanobacteria to humans,onemighthavepredictedagradualplateauingofactivity,butthis wasclearlynotthecase.Importantly,thenewdiscoverieshavecontinuedto comefromspeciesacrossthephylogenetictree,andsothefieldremainstruly interdisciplinary,whichisreflectedintwovolumes,CircadianRhythmsand Biological Clocks Part A and B. Wecontinuetoseeadvancesinthemethodsusedtomeasureandanalyze rhythms,to identifynew circadiangenes,andto characterizeknown clock components. In fact, clocks are now being modulated with a goal of ther- apeutic application. At the same time, there is considerable focus on the molecularmechanismsthroughwhichrhythmsaretransmittedbytheclock. Majorclockproteinsaretranscriptionfactorsthateffectivelydriverhythmic expression of many genes, which generally vary from tissue to tissue. The mechanism by which such rhythmic transcription occurs is a subject of intense investigation, and sophisticated techniques have been brought to bearonit.However,itisalsoevidentthatposttranscriptionalorevenpost- translational mechanisms alone can drive the cycling of RNA or protein. Indeed,proteinsmaynotevenneedtocycleintermsoflevelsastheiractivity canberegulatedthroughcyclicmodifications,suchasphosphorylation.Sev- eralclockproteinsarekinases,andincyanobacteria,theentireclockcanbe reconstituted as a rhythmic phosphorylation cycle. In addition, 24-h oscil- lations that are independent not only of transcription but also of known clock elements have been proposed for redox pathways in the cell. Thus, whilegenome-wideanalysesareallowingidentificationofRNAsexpressed rhythmicallyindifferenttissues,andeveninsmallgroupsofbrainneurons, proteomicstudieshavebeeninitiatedtopinpointrhythmsatthislevel.Allof these have required development and use of the appropriate, anatomical, molecular, biochemical, and statistical tools described here. Rhythmsinmoleculesleadtorhythmsincellularandorganismalphys- iology.Asclocksarefoundthroughoutthebody,theycontrolmanyphys- iologicalprocessesandbehaviors.Inthebrain,rhythmsofelectricalactivity xvii xviii Preface aresynchronizedacrossclockcellsandtransmittedacrosscircadiancircuits, likely comprised of neurons and glia, to generate rhythmic behavior. Cel- lularrhythms,suchasinmitochondrialrespiration,mayoccurineverycell in mammals. In addition, each organ/system, such as the cardiovascular system,hasitsowncircadianphysiologythatcanbemeasuredthroughappli- cation of specific methods. Interestingly, while the light:dark cycle is the most powerful entraining stimulus for the clock in the brain, which then synchronizes other body clocks, rhythmic gene expression in peripheral tissues like the liver responds most strongly to the time of feeding. Thus, aberrant feeding schedules can have adverse effects on metabolic function, but the time of feeding can even be manipulated to produce beneficial consequences. Overall, it is increasingly evident that circadian rhythms are critical for organismalfitness.Severalapproachesarenowbeingusedtoassesscircadian functioninhumans,itscontrolbygeneticfactors,anditsrelevancetohuman health.Disruptedrhythmshavebeenassociatedwithneurologicalandpsy- chiatricdisordersandstudiesarenowunderwaytoaddressthesignificanceof suchassociation.Thesevolumesprovidesmethodologicalinsightintocirca- dian physiology and behavior in model organisms and in humans and touches upon the pathological implications of circadian dysfunction. While I took on the job of putting these volumes together, the actual creditshouldgotoallthecontributingauthors,whotooktimeoutoftheir extremelybusylivestomakethevolumerepresentativeofthebestworkin the circadian field. Iam incrediblygrateful for their efforts andtheir coop- eration.Also,allofthiswasmadepossiblebytheconstanthelpofEditorial ProjectManager,SarahLay,whowasarealpleasuretoworkwiththrough- out the process. AMITA SEHGAL CHAPTER ONE Studying Circadian Rhythm and Sleep Using Genetic Drosophila Screens in Sofia Axelrod, Lino Saez, Michael W. Young1 LaboratoryofGenetics,TheRockefellerUniversity,NewYork,USA 1Correspondingauthor:e-mailaddress:[email protected] Contents 1. Introduction:StudyingCircadianBehaviorintheFruitFly,Drosophilamelanogaster 4 2. ScreeningforCircadianRhythmandSleepMutants 5 2.1 Historyofcircadianrhythmscreens 5 2.2 Historyofsleepscreens 7 3. ScreeningTechniques 10 3.1 EMSmutagenesis 10 3.2 Transposonmutagenesis 12 3.3 Toolsforconditionaltransgeneexpression 13 3.4 DrosophilaRNAilibrariesandscreens 14 3.5 AdvantagesanddrawbacksofscreeningwithRNAiincomparisontochemical andtransposonmutagenesis 19 Acknowledgments 21 References 22 Abstract ThepowerofDrosophilamelanogasterasamodelorganismliesinitsabilitytobeused forlarge-scalegeneticscreenswiththecapacitytouncoverthegeneticbasisofbiolog- icalprocesses.Inparticular,geneticscreensforcircadianbehavior,whichhavebeenper- formed since 1971, allowed researchers to make groundbreaking discoveries on multiplelevels:theydiscoveredthatthereisageneticbasisforcircadianbehavior,they identifiedtheso-calledcoreclockgenesthatgovernthisprocess,andtheystartedto paint a detailed picture of the molecular functions of these clock genes and their encodedproteins.Sincethediscoverythatfruitfliessleepin2000,researchershavesuc- cessfullybeenusinggeneticscreeningtoelucidatethemanyquestionssurrounding this basic animal behavior. In this chapter, we briefly recall the history of circadian rhythm and sleep screens and then move on to describe techniques currently employed for mutagenesis and genetic screening in the field. The emphasis lies on comparing the newer approaches of transgenic RNA interference (RNAi) to classical formsofmutagenesis,inparticularintheirapplicationtocircadianbehaviorandsleep. MethodsinEnzymology,Volume551 #2015ElsevierInc. 3 ISSN0076-6879 Allrightsreserved. http://dx.doi.org/10.1016/bs.mie.2014.10.026
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