Circadian Rhythms and Biological Clocks Part A,

460 Pages·2015·15.438 MB·English

by  Sehgal, Amita

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
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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
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