Epigenetic Reprogramming During Mouse Embryogenesis: Methods and Protocols

320 Pages·2021·10.824 MB·English

by  Katia Ancelin, Maud Borensztein

Methods in
Molecular Biology 2214
Katia Ancelin
Maud Borensztein Editors
Epigenetic
Reprogramming
During Mouse
Embryogenesis
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences,
University ofHertfordshire,
Hatfield, Hertfordshire, UK
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Epigenetic Reprogramming
During Mouse Embryogenesis
Methods and Protocols
Edited by
Katia Ancelin
Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris,
France
Maud Borensztein
Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris,
France; Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
Editors
KatiaAncelin MaudBorensztein
InstitutCurie,CNRSUMR3215/ InstitutCurie,CNRSUMR3215/INSERMU934
INSERMU934 ParisSciences&LettresResearch
ParisSciences&LettresResearch University(PSL)
University(PSL) Paris,France
Paris,France
InstitutdeGe´ne´tiqueMole´culairedeMontpellier
UnivMontpellier,CNRS
Montpellier,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-0957-6 ISBN978-1-0716-0958-3 (eBook)
https://doi.org/10.1007/978-1-0716-0958-3
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Preface
Epigenetic reprogramming is crucial for mammalian development and entails unique
changes in the spatial and functional organization of the chromatin landscape. Genome-
wide reprogramming occurs at specific developmental stages, in the germline and early
embryo,andiscriticalforgeneratingatotipotent/pluripotentstate.Altogether,chromatin
remodelingisessentialfor thetransmissionofinformationfromparenttooffspring.
The scarcity of early embryos and germ cells and limited access to these materials
represent considerable challenges for exploring the diversity of genome-wide chromatin
reprogrammingevents.However,constanttechnologicaldevelopmenthasmadeitincreas-
inglypossibletoovercomethisbarrier,therebyleadingtomajorprogress,inparticularusing
themousemodel.Thisbookprovidesanoverviewofthecutting-edgemethodsavailableto
understand chromatin reprogramming in embryos and germ cells. Various and robust
culturesystemsarepresentedwhichconstituteinvaluabletoolstoinvestigatethesedevelop-
mental processes. In parallel, the advent of CRISPR/Cas9-mediated genome modification
and cloning has enabled the identification of new factors involved in reprogramming.
Historically,microscopy-basedapproacheshavealsorevealedtheextentofchromatinrepro-
gramming,andwereviewheredifferentmethodsfordirectexaminationofDNA,RNA,and
proteinsinembryos.Thebookalsoincludesavarietyoflow-inputandsingle-cellassaysfor
exploringthesefeaturesatthegenome-widescale.
Although optimized for mouse embryos, these protocols can be adapted to other
mammalian models and organoids in culture. Ultimately, this volume aims to present a
comprehensive overview of the methods available to scientists wishing to make new dis-
coveriesinthefascinatingfieldofchromatinreprogramming.
Paris,France KatiaAncelin
MaudBorensztein
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 ExVivoCultureforPreimplantationMouseEmbryotoAnalyze
Pluripotency............................................................ 1
KatiaBoutourlinsky,NicolasAlle`gre,andClaireChazaud
2 MicrofabricatedDeviceforHigh-ResolutionImaging
ofPreimplantationEmbryos ............................................. 11
SandrineVandormael-Pournin,EmmanuelFrachon,
SamyGobaa,andMichelCohen-Tannoudji
3 InVitroCultureofMouseBlastocyststotheEggCylinderStage
viaMuralTrophectodermExcision........................................ 31
HaticeO.OzguldezandIvanBedzhov
4 SpatiallyOrganizedDifferentiationofMousePluripotentStem
CellsonMicropatterned Surfaces ......................................... 41
SophieM.MorganiandAnna-KaterinaHadjantonakis
5 MousePrimordialGermCells:InVitroCultureandConversion
toPluripotentStemCellLines............................................ 59
MalgorzataBorkowskaandHarryG.Leitch
6 GenerationofPrimordialGermCell-likeCellsonSmallandLarge
Scales.................................................................. 75
WolframH.GruhnandUfukGu¨nesdogan
7 Genome-ScaleCRISPRScreeningforRegulatorsofCellFate
Transitions............................................................. 91
ValentinaCarlini,KristjanH.Gretarsson,andJamieA.Hackett
8 SomaticReprogramingbyNuclearTransfer................................ 109
VincentBrochardandNathalieBeaujean
9 TargetedTransgenicMiceUsingCRISPR/Cas9Technology ................ 125
FatimaElMarjou,ColinJouhanneau,andDenisKrndija
10 Whole-MountImmunofluorescenceStainingofEarlyMouse
Embryos............................................................... 143
FrederickC.K.Wong
11 InvestigatingtheInnerCellMassoftheMouseBlastocyst
byCombinedImmunofluorescenceStainingandRNAFluorescence
InSituHybridization.................................................... 157
MaudBorensztein
12 MappingofChromosomeTerritoriesby3D-ChromosomePainting
DuringEarlyMouseDevelopment........................................ 175
KatiaAncelin,YusukeMiyanari,OlivierLeroy,
Maria-ElenaTorres-Padilla,andEdithHeard
vii
viii Contents
13 DecipheringtheEarlyMouseEmbryoTranscriptome
byLow-InputRNA-Seq................................................. 189
RaquelPe´rez-Palacios,PatriciaFauque,Aure´lieTeissandier,
andDe´borahBourc’his
14 StudyingDNAMethylationGenome-WidebyBisulfiteSequencing
fromLowAmountsofDNAinMammals.................................. 207
AmbreBender,HalaAlAdhami,ThomasDahlet,
andMichaelWeber
15 ProfilingDNAMethylationGenome-WideinSingleCells................... 221
Ant(cid:1)onioGalva˜oandGavinKelsey
16 TrackingHistoneModificationsinEmbryosandLow-InputSamples
UsingUltrasensitiveSTARChIP-Seq ..................................... 241
BingjieZhang,XuPeng,FengXu,andWeiXie
17 ChromatinProfilinginMouseEmbryonicGermCellsbyCUT&RUN........ 253
SrinivasaAbishekPrakashandJoanBarau
18 DamIDtoMapGenome-ProteinInteractionsinPreimplantation
MouseEmbryos........................................................ 265
MrinmoyPal,JopKind,andMaria-ElenaTorres-Padilla
19 UnderstandingChromosomeStructureDuringEarlyMouse
DevelopmentbyaSingle-CellHi-CAnalysis............................... 283
Noe´mieRanisavljevic,MaudBorensztein,andKatiaAncelin
20 BioinformaticAnalysisofSingle-CellHi-CDatafromEarlyMouse
Embryo ............................................................... 295
SamuelCollombet,YuviaA.Pe´rez-Rico,KatiaAncelin,
NicolasServant,andEdithHeard
Index ...................................................................... 317
Contributors
HALA ALADHAMI • CNRSUMR7242,BiotechnologyandCellSignaling,Universityof
Strasbourg,IllkirchCedex,France
NICOLAS ALLE`GRE • InstitutGReD,Universite´ClermontAuvergne,CNRS,Inserm,
Clermont-Ferrand,France
KATIAANCELIN • InstitutCurie,CNRSUMR3215/INSERMU934,ParisSciences&
LettresResearchUniversity(PSL),Paris,France
JOANBARAU • InstituteofMolecularBiology(IMB),Mainz,Germany
NATHALIEBEAUJEAN • Universite´Paris-Saclay,INRAE,ENVA,BREEDU1198,Jouy-en-
Josas,France;UnivLyon,Universite´Lyon1,Inserm,INRAE,StemCellandBrain
ResearchInstituteU1208,USC1361,Bron,France
IVANBEDZHOV • EmbryonicSelf-OrganizationResearchGroup,MaxPlanckInstitutefor
MolecularBiomedicine,Mu¨nster,Germany
AMBREBENDER • CNRSUMR7242,BiotechnologyandCellSignaling,Universityof
Strasbourg,IllkirchCedex,France
MAUDBORENSZTEIN • InstitutCurie,CNRSUMR3215/INSERMU934,ParisSciences&
LettresResearchUniversity(PSL),Paris,France;InstitutdeGe´ne´tiqueMole´culairede
Montpellier,UnivMontpellier,CNRS,Montpellier,France
MALGORZATABORKOWSKA • MRCLondonInstituteofMedicalSciences(LMS),London,UK;
InstituteofClinicalSciences(ICS),FacultyofMedicine,ImperialCollegeLondon,London,
UK
DE´BORAHBOURC’HIS • InstitutCurie,INSERMU934,CNRSUMR3215,ParisSciences
LettresResearchUniversity,Paris,France
KATIABOUTOURLINSKY • InstitutGReD,Universite´ClermontAuvergne,CNRS,Inserm,
Clermont-Ferrand,France
VINCENTBROCHARD • Universite´Paris-Saclay,INRAE,ENVA,BREEDU1198,Jouy-en-
Josas,France
VALENTINACARLINI • EpigeneticsandNeurobiologyUnit,EuropeanMolecularBiology
Laboratory(EMBL),Rome,Italy;CollaborationforJointPhDDegreebetweenEMBLand
HeidelbergUniversity,FacultyofBiosciences,Heidelberg,Germany
CLAIRECHAZAUD • InstitutGReD,Universite´ClermontAuvergne,CNRS,Inserm,
Clermont-Ferrand,France
MICHELCOHEN-TANNOUDJI • EarlyMammalianDevelopmentandStemCellBiology,
InstitutPasteur,CNRSUMR3738,Paris,France
SAMUELCOLLOMBET • InstitutCurie,CNRSUMR3215/INSERMU934,ParisSciences&
LettresResearchUniversity(PSL),Paris,France;EMBL,Heidelberg,Germany
THOMASDAHLET • CNRSUMR7242,BiotechnologyandCellSignaling,Universityof
Strasbourg,IllkirchCedex,France
FATIMAELMARJOU • CellMigrationandInvasionGroup,DepartmentofCellBiology,
UMR144,InstitutCurie,Paris,France
ix
x Contributors
PATRICIAFAUQUE • LaboratoiredeBiologiedelaReproduction,HoˆpitalFranc¸ois
Mitterrand,Universite´deBourgogne,Dijon,France;INSERMUMR1231,Universite´de
BourgogneFranche-Comte´,Dijon,France
EMMANUELFRACHON • GroupofBiomaterialsandMicrofluidicsCoreFacility,Institut
Pasteur,Paris,France
ANTO´NIO GALVA˜O • InstituteofAnimalReproductionandFoodResearchofPAS,Olsztyn,
Poland;EpigeneticsProgramme,TheBabrahamInstitute,Cambridge,UK;Centrefor
TrophoblastResearch,UniversityofCambridge,Cambridge,UK
SAMYGOBAA • GroupofBiomaterialsandMicrofluidicsCoreFacility,InstitutPasteur,
Paris,France
KRISTJANH.GRETARSSON • EpigeneticsandNeurobiologyUnit,EuropeanMolecularBiology
Laboratory(EMBL),Rome,Italy
WOLFRAMH.GRUHN • WellcomeTrust/CancerResearchUKGurdonInstitute,University
ofCambridge,Cambridge,UK;DepartmentofPhysiology,DevelopmentandNeuroscience,
UniversityofCambridge,Cambridge,UK
UFUKGU¨NESDOGAN • DepartmentofDevelopmentalBiology,Go¨ttingenCenter for
MolecularBiosciences,UniversityofGo¨ttingen,Go¨ttingen,Germany;Departmentof
MolecularDevelopmentalBiology,MaxPlanckInstituteforBiophysicalChemistry,
Go¨ttingen,Germany
JAMIE A.HACKETT • EpigeneticsandNeurobiologyUnit,EuropeanMolecularBiology
Laboratory(EMBL),Rome,Italy
ANNA-KATERINAHADJANTONAKIS • DevelopmentalBiologyProgram,SloanKettering
Institute,MemorialSloanKetteringCancerCenter,NewYork,NY,USA
EDITHHEARD • EMBL,Heidelberg,Germany;InstitutCurie,CNRSUMR3215/INSERM
U934,ParisSciences&LettresResearchUniversity(PSL),Paris,France
COLINJOUHANNEAU • InstitutCuriePlateforme d’Expe´rimentationInVivo,Universite´
Paris-Sud11,Orsay,France
GAVINKELSEY • EpigeneticsProgramme,TheBabrahamInstitute,Cambridge,UK;Centre
forTrophoblastResearch,UniversityofCambridge,Cambridge,UK
JOPKIND • OncodeInstitute,HubrechtInstitute–KNAWandUniversityMedicalCenter
Utrecht,Utrecht,TheNetherlands
DENIS KRNDIJA • CellMigrationandInvasionGroup,DepartmentofCellBiology,
UMR144,InstitutCurie,Paris,France
HARRYG.LEITCH • MRCLondonInstituteofMedicalSciences(LMS),London,UK;
InstituteofClinicalSciences(ICS),FacultyofMedicine,ImperialCollegeLondon,London,
UK
OLIVIER LEROY • InstitutCurie,CNRSUMR3215/INSERMU934,ParisSciences&
LettresResearchUniversity(PSL),Paris,France
YUSUKEMIYANARI • DivisionofNuclearDynamics,ExploratoryResearchCenteronLifeand
LivingSystems:ExCELLSNationalInstituteforBasicBiology,Okazaki,Japan
SOPHIEM.MORGANI • DevelopmentalBiologyProgram,SloanKetteringInstitute,Memorial
SloanKetteringCancerCenter,NewYork,NY,USA;Wellcome-MRCCambridgeStem
CellInstitute,UniversityofCambridge,Cambridge,UK
HATICEO.OZGULDEZ • EmbryonicSelf-OrganizationResearchGroup,MaxPlanck
InstituteforMolecularBiomedicine,Mu¨nster,Germany
MRINMOYPAL • InstituteofEpigeneticsandStemCells(IES),HelmholtzZentrumMu¨nchen,
Munich,Germany