Vertebrate Embryogenesis: Embryological, Cellular, and Genetic Methods

434 Pages·2019·10.24 MB·English

by  Francisco J. Pelegri

Methods in
Molecular Biology 1920
Francisco J. Pelegri Editor
Vertebrate
Embryogenesis
Embryological, Cellular, and
Genetic Methods
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Vertebrate Embryogenesis
Embryological, Cellular, and Genetic Methods
Second Edition
Edited by
Francisco J. Pelegri
Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
Editor
FranciscoJ.Pelegri
LaboratoryofGenetics
UniversityofWisconsin–Madison
Madison,WI,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9008-5 ISBN978-1-4939-9009-2 (eBook)
https://doi.org/10.1007/978-1-4939-9009-2
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Preface
Despitecontinuousandfast-pacedprogress,muchremainsunknowninourunderstanding
ofbiologicalprocesses.Noexceptionisthefieldofanimalembryogenesis,evenasthisfield
was one of the earliest to gain attention with detailed genetic, cellular, and molecular
analyses. This is particularly true for vertebrate species, due to their relative intractability
comparedtoinvertebrates.Yetvertebratesystems,andtheirearlieststagesofdevelopment,
continuetobothcapturetheattentionandimaginationofscientistsworldwide.Duetothe
conservation of cellular and signaling pathways, the study of animal embryogenesis also
providesvaluableentrypointsintoprocessesactingthroughtherestoforganismaldevelop-
mentandcellularhomeostasis.
Within vertebrates, a small number of model systems have provided a wealth of infor-
mation.Theseselectfew,includingamphibianssuchastheAfricantoadXenopuslaevis,the
chick,mice,andlater thezebrafish,haveactedaspillarsthathaveallowedthedevelopment
of unifying hypotheses. As this general approach expands our platforms of knowledge,
additional vertebrate species are being used to support or challenge those hypotheses. For
example,wefindthatfeaturesofmanymodelsystems,suchasrapiddevelopmentaltimeand
large fecundity rates, may reflect specialized adaptations, some of which may be unique to
specificphylogeneticbranches.Lessfecundspecies,whichareoftenlessconvenienttousein
alaboratorysetting,mayrepresentbiologicalmechanismsandconditionsthatmaybemore
widely conserved. We realize that our knowledge of animal processes is patchy, following
lone branches separated from others by millions of years’ worth of evolutionary changes.
Cellularsystems,signalingpathways,andmoleculesareconservedandshared,butthereare
innumerable differences that in our broad strokes picture appear saltatory. Given this
structure of knowledge, the precise gradation of changes from one species to the other is
attimeshardtodiscern.
These gaps in knowledge are increasingly being addressed through the study of other,
nontraditional vertebrate species. Nontraditional vertebrate model systems have also
recently gathered tremendous momentum through the development of readily implemen-
ted gene editing tools, such as CRISPR-Cas9. This new technology enables targeted
changes to the genome and is especially useful for generating loss of function conditions
toassessgenefunction.Thelimitsofourknowledgearenolongersetbyhighfecundityand
short generation time, and any organism that can be bred under controlled conditions is
nowaccessiblefor thegeneticanalysisofendogenousfunctionsandmechanisms.
Thisvolumehasbeencompiledwithinthiscontextandaccordinglyrepresentsacontin-
uumbetweenthetraditionalmodelorganismsandnewmethodologiesandmodelsystems.
Improved protocols with updated advances in key traditional model systems are included,
such as in amphibians, chicken, mouse, and zebrafish. Within these traditional model
systems, new developments are presented, such as protocols for the analysis of cellular
membranes and intracellular signals, light-controlled manipulation of function, and the
analysis of transcriptomic and proteomic data in the context of the embryo. Additional
systemsaredescribed,includingtheleopardgeckoandtheflexible-shelledslider turtle.
Several other timely topics relevant to vertebrate embryogenesis are presented in this
volume.Recentstudieshavehighlightedtheimportanceofmembrane-lesscompartmentsas
cellular functional hubs in the embryo. In this volume, a series of chapters addresses the
v
vi Preface
visualizationand characterization ofthebalbianibody,amembrane-lessstructure involved
intheoocyteandprimordialgermcelldevelopment.Anadditionalsetofchaptersaddresses
reproductivetechnologiesforgenefunctionassessmentandgermlinemanipulation,suchas
interspecieshybridproduction,germlinetransplantation,andsomaticcellnuclear transfer.
Anotherchapterprovidesasimpleprotocolfortheinductionofgene-inactivatingCRISPR-
Cas9-mediated mutations. As a presage to a future with an increasing contribution of
mathematical analysis to developmental and cellular biology, a chapter includes detailed
directionsto modelcelldivisionpatternsinearly embryos.Finally, thisvolume includesan
updatedchapterontheresponsiblecareanduseofvertebrateanimalsinalaboratorysetting.
As with the first edition of this series, this volume is meant to foster cross-model work
andideasbypresentingmethodsthatcanbeappliedacrosslaboratoriesandspeciesbound-
aries. We are also delighted to present chapters on new model systems. We hope that this
workwillbeusefultoscientists,educators,andtheadvancedgeneralaudienceandwillactas
aninspirationtofurtheranunderstandingandappreciationofanimaldevelopment.
Madison,WI FranciscoJ.Pelegri
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 CultureandHostTransferofXenopusOocytesforMaternal
mRNADepletionandGenomeEditingExperiments........................ 1
DouglasW.Houston
2 ImmunofluorescenceofMicrotubuleAssembliesinAmphibian
OocytesandEarlyEmbryos.............................................. 17
ThaoNguyen,TimothyJ.Mitchison,andMartinWu¨hr
3 AssayingNanoLucLuciferaseActivityfrommRNA-Injected
XenopusEmbryos....................................................... 33
MichaelD.Sheets
4 ReconstitutionofIntracellularCalciumSignaling
inXenopusEggExtracts ................................................. 41
AlexanderA.TokmakovandKen-IchiSato
5 MembraneMicrodomainsasPlatformtoStudyMembrane-Associated
EventsDuringOogenesis,MeioticMaturation,andFertilization
inXenopuslaevis........................................................ 59
Ken-IchiSatoandAlexanderA.Tokmakov
6 EmbryologicalandGeneticManipulationofChickDevelopment............. 75
LauraS.Gammill,BridgetJacques-Fricke,andJulaineRoffers-Agarwal
7 IdentifyingProtein-DNAandProtein-ProteinInteractions
inAvianEmbryos....................................................... 99
AnaPaulaAzambujaandMarcosSimoes-Costa
8 ExperimentalManipulationofPloidyinZebrafishEmbryos
andItsApplicationinGeneticScreens..................................... 111
TriveniMenonandSreelajaNair
9 RNATomographyforSpatiallyResolvedTranscriptomics(Tomo-Seq)........ 129
KarolineHollerandJanPhilippJunker
10 OptogeneticControlofSubcellularProteinLocation
andSignalinginVertebrateEmbryos...................................... 143
ClareE.Buckley
11 ExUteroCultureandImagingofMouseEmbryos ......................... 163
SonjaNowotschin,VidurGarg,AnnaPiliszek,andAnna-Katerina
Hadjantonakis
12 DetectionofGeneandProteinExpressioninMouseEmbryos
andTissueSections ..................................................... 183
EdwinaMcGlinn,MiriamA.Holzman,andJenniferH.Mansfield
13 ReptileEmbryologyandRegeneration .................................... 219
MatthewK.VickaryousandEmilyA.B.Gilbert
vii
viii Contents
14 ManipulationofDevelopmentalFunctioninTurtles
withNotesonAlligators................................................. 247
JacquelineE.Moustakas-Verho,RebeccaMcLennan,JenniferSpengler,
PaulM.Kulesa,andJudithA.Cebra-Thomas
15 MethodsforIsolatingtheBalbianiBody/Germplasm
fromXenopuslaevisOocytes ............................................. 265
AmandaButler,DawnOwens,MaryLouKing,andTristanAguero
16 VisualizingtheBalbianiBodyinZebrafishOocytes ......................... 277
KathyAnnL.LeeandFlorenceL.Marlow
17 IsolationofZebrafishBalbianiBodiesforProteomicAnalysis ................ 295
AllisonJamieson-LucyandMaryC.Mullins
18 GenerationofXenopusHaploid,Triploid,andHybridEmbryos.............. 303
RomainGibeauxandRebeccaHeald
19 GermCellTransplantationinAvianSpecies................................ 317
YoungHyunPark,YoungMinKim,andJaeYongHan
20 ProductionofGerm-LineChimerasinZebrafish ........................... 327
TaijuSaito,RieGoto,NicolaRivers,andEtsuroYamaha
21 AMethodforZebrafishFollicleTransplantation
intoRecipientMothersfor theGenerationofFertilizableEggs
andViableOffspring.................................................... 343
ZsoltCsenkiandFerencMueller
22 OptimizedProtocolofZebrafishSomaticCellNuclear
Transfer(SCNT)........................................................ 353
SukumalPrukudom,KannikaSiripattarapravat,WilliamPoulos,
andJoseB.Cibelli
23 AnAccessibleProtocolfor theGenerationofCRISPR-Cas9
KnockoutsUsingINDELsinZebrafish.................................... 377
CaraE.MoravecandFranciscoJ.Pelegri
24 ModelingEmbryonicCleavagePatterns................................... 393
DmitryErshovandNicolasMinc
25 LaboratoryGuidelinesforAnimalCare.................................... 407
MarceloCoutoandCharlesCates
Index ...................................................................... 431
Contributors
TRISTANAGUERO (cid:1) DepartmentofCellBiology,MillerSchoolofMedicine,Universityof
Miami,Miami,FL,USA;DepartmentofDevelopmentalBiology,INSIBIO(CONICET-
TucumanNationalUniversity),Tucuman,Argentina
ANAPAULAAZAMBUJA (cid:1) DepartmentofMolecularBiologyandGenetics,CornellUniversity,
Ithaca,NY,USA
CLAREE.BUCKLEY (cid:1) DepartmentofPhysiology,DevelopmentandNeuroscience,Universityof
Cambridge,Cambridge,UK
AMANDABUTLER (cid:1) DepartmentofCellBiology,MillerSchoolofMedicine,Universityof
Miami,Miami,FL,USA
CHARLESCATES (cid:1) Cedars-SinaiMedicalCenter,LosAngeles,CA,USA
JUDITHA.CEBRA-THOMAS (cid:1) BiologyDepartment,MillersvilleUniversity,Millersville,PA,
USA
JOSEB.CIBELLI (cid:1) DepartmentofAnimalScience,MichiganStateUniversity,EastLansing,
MI,USA;LargeAnimalClinicalSciencesDepartment,MichiganStateUniversity,East
Lansing,MI,USA
MARCELOCOUTO (cid:1) DavidGeffenSchoolofMedicine,UCLA,LosAngeles,CA,USA
ZSOLTCSENKI (cid:1) FacultyofAgriculturalandEnvironmentalSciences,Departmentof
Aquaculture,InstituteofAquacultureandEnvironmentalSafety,SzentIstva´nUniversity,
Go¨do¨ll˝o,Hungary
DMITRYERSHOV (cid:1) InstitutJacquesMonod,CNRSUMR7592,Paris,France;Universite´
ParisDiderot,Paris,France
LAURA S.GAMMILL (cid:1) DepartmentofGenetics,CellBiologyandDevelopment,Universityof
Minnesota,Minneapolis,MN,USA
VIDURGARG (cid:1) DevelopmentalBiologyProgram,SloanKetteringInstitute,MemorialSloan
KetteringCancerCenter,NewYork,NY,USA
ROMAINGIBEAUX (cid:1) DepartmentofMolecularandCellBiology,UniversityofCalifornia,
Berkeley,CA,USA
EMILYA.B.GILBERT (cid:1) DepartmentofBiomedicalSciences,UniversityofGuelph,Guelph,
ON,Canada;DepartmentofSurgery,DonnellyCentreforCellularandBiomolecular
Research,UniversityofToronto,Toronto,ON,Canada
RIEGOTO (cid:1) SouthEhimeFisheriesResearchCenter,EhimeUniversity,Ehime,Japan
ANNA-KATERINAHADJANTONAKIS (cid:1) DevelopmentalBiologyProgram,SloanKettering
Institute,MemorialSloanKetteringCancerCenter,NewYork,NY,USA
JAEYONGHAN (cid:1) DepartmentofAgriculturalBiotechnologyandResearchInstituteof
AgricultureandLifeSciences,CollegeofAgricultureandLifeSciences,SeoulNational
University,Seoul,Korea
REBECCA HEALD (cid:1) DepartmentofMolecularandCellBiology,UniversityofCalifornia,
Berkeley,CA,USA
KAROLINEHOLLER (cid:1) BerlinInstituteforMedicalSystemsBiology,MDCBerlin,Berlin,
Germany
MIRIAMA.HOLZMAN (cid:1) DepartmentofBiology,BarnardCollege,ColumbiaUniversity,New
York,NY,USA
DOUGLASW.HOUSTON (cid:1) DepartmentofBiology,TheUniversityofIowa,IowaCity,IA,USA
ix
x Contributors
BRIDGET JACQUES-FRICKE (cid:1) DepartmentofGenetics,CellBiologyandDevelopment,
UniversityofMinnesota,Minneapolis,MN,USA;DepartmentofBiology,Hamline
University,SaintPaul,MN,USA
ALLISON JAMIESON-LUCY (cid:1) DepartmentofCellandDevelopmentalBiology,PerelmanSchool
ofMedicine,UniversityofPennsylvania,Philadelphia,PA,USA
JANPHILIPPJUNKER (cid:1) BerlinInstituteforMedicalSystemsBiology,MDCBerlin,Berlin,
Germany
YOUNGMINKIM (cid:1) DepartmentofAgriculturalBiotechnologyandResearchInstituteof
AgricultureandLifeSciences,CollegeofAgricultureandLifeSciences,SeoulNational
University,Seoul,Korea
MARYLOUKING (cid:1) DepartmentofCellBiology,MillerSchoolofMedicine,Universityof
Miami,Miami,FL,USA
PAULM.KULESA (cid:1) StowersInstituteforMedicalResearch,KansasCity,MO,USA;
DepartmentofAnatomyandCellBiology,UniversityofKansasSchoolofMedicine,Kansas
City,KS,USA
KATHYANNL.LEE (cid:1) DepartmentofCellDevelopmentalandRegenerativeBiology,Icahn
SchoolofMedicineatMountSinai,NewYork,NY,USA
JENNIFERH.MANSFIELD (cid:1) DepartmentofBiology,BarnardCollege,ColumbiaUniversity,
NewYork,NY,USA
FLORENCEL.MARLOW (cid:1) DepartmentofCellDevelopmentalandRegenerativeBiology,Icahn
SchoolofMedicineatMountSinai,NewYork,NY,USA
EDWINAMCGLINN (cid:1) EMBLAustralia,AustralianRegenerativeMedicineInstitute,Monash
University,Clayton,VIC,Australia
REBECCA MCLENNAN (cid:1) StowersInstituteforMedicalResearch,KansasCity,MO,USA
TRIVENI MENON (cid:1) DepartmentofBiologicalSciences,TataInstituteofFundamental
Research,Mumbai,India
NICOLASMINC (cid:1) InstitutJacquesMonod,CNRSUMR7592,Paris,France;Universite´Paris
Diderot,Paris,France
TIMOTHYJ.MITCHISON (cid:1) DepartmentofSystemsBiology,HarvardMedicalSchool,Boston,
MA,USA
CARAE.MORAVEC (cid:1) LaboratoryofGenetics,UniversityofWisconsin–Madison,Madison,WI,
USA
JACQUELINEE.MOUSTAKAS-VERHO (cid:1) InstituteofBiotechnology,UniversityofHelsinki,
Helsinki,Finland;FacultyofBiologicalandEnvironmentalSciences,Universityof
Helsinki,Helsinki,Finland
FERENCMUELLER (cid:1) InstituteofCancerandGenomicSciences,CollegeofMedicalandDental
Sciences,UniversityofBirmingham,Birmingham,UK
MARYC.MULLINS (cid:1) DepartmentofCellandDevelopmentalBiology,PerelmanSchoolof
Medicine,UniversityofPennsylvania,Philadelphia,PA,USA
SREELAJANAIR (cid:1) DepartmentofBiologicalSciences,TataInstituteofFundamentalResearch,
Mumbai,India
THAONGUYEN (cid:1) Lewis-SiglerInstituteforIntegrativeGenomicsandDepartmentof
MolecularBiology,PrincetonUniversity,Princeton,NJ,USA
SONJANOWOTSCHIN (cid:1) DevelopmentalBiologyProgram,SloanKetteringInstitute,Memorial
SloanKetteringCancerCenter,NewYork,NY,USA
DAWNOWENS (cid:1) DepartmentofCellBiology,MillerSchoolofMedicine,UniversityofMiami,
Miami,FL,USA