Nuclear, Chromosomal, and Genomic Architecture in Biology and Medicine

657 Pages·2022·22.186 MB·English

by  Malgorzata Kloc, Jacek Z. Kubiak

Results and Problems in Cell Differentiation 70
Malgorzata Kloc
Jacek Z. Kubiak   Editors
Nuclear,
Chromosomal, and
Genomic Architecture
in Biology and
Medicine
Results and Problems in Cell Differentiation
Volume 70
SeriesEditors
JacekZ.Kubiak,Rennes,France
MalgorzataKloc,Houston,TX,USA
Results and Problems in Cell Differentiation is an up-to-date book series that
presents and explores selected questions of cell and developmental biology. Each
volumefocusesonasingle,well-definedtopic.Reviewsaddressbasicquestionsand
phenomena, but also provide concise information on the most recent advances.
Together,thevolumesprovideavaluableoverviewofthisexcitinganddynamically
expandingfield.ThisseriesisindexedinPubMed.
(cid:129)
Malgorzata Kloc Jacek Z. Kubiak
Editors
Nuclear, Chromosomal,
and Genomic Architecture
in Biology and Medicine
Editors
MalgorzataKloc JacekZ.Kubiak
TransplantImmunology InstituteofGeneticsandDevelopmentofRennes
TheHoustonMethodistResearchInstitute CNRS
Houston,TX,USA UniversitédeRennes
Rennes,France
ISSN0080-1844 ISSN1861-0412 (electronic)
ResultsandProblemsinCellDifferentiation
ISBN978-3-031-06572-9 ISBN978-3-031-06573-6 (eBook)
https://doi.org/10.1007/978-3-031-06573-6
©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicensetoSpringerNatureSwitzerland
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Preface
The volume reviews the current knowledge and hypotheses on the genome, chro-
matin,chromosome,centromere,andnucleolusarchitecture,organization,andevo-
lution. It also describes how the changes in the structure, nuclear actin dynamics,
mechanosensory, and epigenetic modifications affect cell fate, development, and
health.Becauseallthesestructuresandprocessesarephysicallyandmechanistically
interconnected, and it is impossible to describe them as independent units, the
readers should be aware that the following partitioning of the volume content is
very arbitrary. The first part of this volume presents hypotheses and models of the
genomenano-architecture,spatialorganization,andevolution.Italsodescribeshow
thegenomestructureandmodificationsaffectcellfateanddevelopmentandhowthe
spatial genomic helps understand whole-body diseases and multimorbidity. The
second part is devoted to chromosome, chromatin, and centromere structure, orga-
nization,anddynamicsandhowtheyaffectcellfunctionsanddiseasedevelopment.
The third part reviews how epigenetic modification and mechanosensing regulate
gene expression, cell cycle, functions, and phenotype, and how they contribute to
cancer development. The fourth part describes the architecture and three-
dimensionality of the nucleus, the nucleolar organizer region, and nucleolus, and
how the architectural changes affect health and disease. The fifth part summarizes
our current knowledge on the role of nuclear actin and its dynamics in nuclear
architecture,polarity,andgeneexpression.
Besidesbeinginformativeandscientificallyinspiring, wehopethatthisvolume
will open new avenues for the studies of genomic, chromosomal, and nuclear
architecture and their relevance to the establishment of cell function, fate, and
developmentofdiseases.
Houston,TX MalgorzataKloc
Rennes,France JacekZ.Kubiak
v
Book Abstract
This book reviews the most current knowledge on the structure, architecture,
functions, and evolution of the genome, chromatin, nucleus, and nucleolus and
howtheyaffectcellfateindevelopmentanddiseases.Thebookcoversthefollowing
subjects: the genome architecture, organization, and evolution and their effects on
cell fate; the chromosomes chromatin and centromere properties, architecture, and
dynamics; the mechanosensitive and epigenetic regulators of gene expression and
chromatin organization; the architecture of nucleus, nucleolus, and nucleolar orga-
nizer;theroleofnuclearactininpolarization,genomeorganization,andfunctions.It
alsodescribeshowthearchitecturedisruptionofthesestructuresleadstocancerand
otherdiseases.Thisbookshouldgivethereadersanewperspectiveonthenuclear,
chromosome, and genomic architecture and their importance for evolution and
variouscellfunctions.
vii
Contents
PartI GenomeArchitecture,Evolution,andCellFate
1 NetworksandIslandsofGenomeNano-architectureand
TheirPotentialRelevanceforRadiationBiology. . . . . . . . . . . . . . . 3
MichaelHausmann,GeorgHildenbrand,andGötzPilarczyk
2 AUnifiedGenomicMechanismofCell-FateChange. . . . . . . . . . . . 35
MasaTsuchiya,AlessandroGiuliani,GiovannaZimatore,
JekaterinaErenpreisa,andKenichiYoshikawa
3 AlterationstoGenomeOrganisationinStemCells,Their
DifferentiationandAssociatedDiseases. . . . . . . . . . . . . . . . . . . . . . 71
JoannaM.Bridger,RitaTorresPereira,CristinaPina,SabrinaTosi,
andAnnabelleLewis
4 HowGenomesEmerge,Function,andEvolve:LivingSystems
Emergence—Genotype-Phenotype-Multilism—Genome/Systems
Ecology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
TobiasA.Knoch
5 IntegratingMultimorbidityintoaWhole-BodyUnderstanding
ofDiseaseUsingSpatialGenomics. . . . . . . . . . . . . . . . . . . . . . . . . 157
SreemolGokuladhas,RoanE.Zaied,WilliamSchierding,
SophieFarrow,TayazaFadason,andJustinM.O’Sullivan
PartII ChromosomesandChromatinArchitectureandDynamics
6 MitoticAntipairingofHomologousChromosomes. . . . . . . . . . . . . 191
LisaL.Hua,ChristianJ.Casas,andTakashiMikawa
7 CENP-A:AHistoneH3VariantwithKeyRolesinCentromere
ArchitectureinHealthyandDiseasedStates. . . . . . . . . . . . . . . . . . 221
DanielJeffery,MarinaLochhead,andGenevièveAlmouzni
ix
x Contents
8 ScalingRelationshipinChromatinasaPolymer. . . . . . . . . . . . . . . 263
TakahiroSakaueandAkatsukiKimura
9 ChromatinDynamicsDuringEntrytoQuiescenceand
CompromisedFunctionalityinCancerCells. . . . . . . . . . . . . . . . . . 279
OliviaGraceDobbsandDawnCoverley
10 FunctionalAspectsofSpermChromatinOrganization. . . . . . . . . . 295
JordiRibas-Maynou,HieuNguyen,HongwenWu,
andW.StevenWard
PartIII MechanosensitiveandEpigeneticRegulatorsofGene
ExpressionandChromatinOrganization
11 TheLINCComplexAssiststheNuclearImportof
MechanosensitiveTranscriptionalRegulators. . . . . . . . . . . . . . . . . 315
TomoyoTakataandMikiMatsumura
12 Epigenetic-MediatedRegulationofGeneExpressionfor
BiologicalControlandCancer:CellandTissueStructure,
Function,andPhenotype. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
AndrewJ.Fritz,MohammedElDika,RabailH.Toor,
PrincessD.Rodriguez,StephenJ.Foley,RahimUllah,DaijingNie,
BodhisattwaBanerjee,DorcasLohese,KirstenM.Tracy,
KarenC.Glass,SethFrietze,PrachiN.Ghule,JessicaL.Heath,
AnthonyN.Imbalzano,AndrevanWijnen,JonathanGordon,
JaneB.Lian,JanetL.Stein,andGaryS.Stein
13 Epigenetic-MediatedRegulationofGeneExpressionfor
BiologicalControlandCancer:FidelityofMechanisms
GoverningtheCellCycle. . . .. . . . . .. . . . .. . . . . .. . . . .. . . . . .. 375
MohammedElDika,AndrewJ.Fritz,RabailH.Toor,
PrincessD.Rodriguez,StephenJ.Foley,RahimUllah,DaijingNie,
BodhisattwaBanerjee,DorcasLohese,KirstenM.Tracy,
KarenC.Glass,SethFrietze,PrachiN.Ghule,JessicaL.Heath,
AnthonyN.Imbalzano,AndrevanWijnen,JonathanGordon,
JaneB.Lian,JanetL.Stein,andGaryS.Stein
14 HistoneModificationsinMousePronucleiandConsequences
forEmbryoDevelopment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
EwaBorsuk,JuliaMichalkiewicz,JacekZ.Kubiak,
andMalgorzataKloc
PartIV Nucleus,Nucleolus,andNucleolarOrganizerArchitecture
15 NuclearArchitectureintheNervousSystem. . . . . . . . . . . . . . . . . . 419
KenjiItoandTakumiTakizawa
Contents xi
16 NuclearMorphologicalAbnormalitiesinCancer:ASearch
forUnifyingMechanisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443
IshitaSinghandTanmayP.Lele
17 NuclearOrganizationinResponsetoStress:ASpecialFocus
onNucleoli. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
EnkhzayaBatnasan,SonjaKoivukoski,MinttuKärkkäinen,
andLeenaLatonen
18 SimulationofDifferentThree-DimensionalModelsofWhole
InterphaseNucleiComparedtoExperiments-AConsistent
Scale-BridgingSimulationFrameworkforGenome
Organization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
TobiasA.Knoch
19 NucleolarOrganizerRegionsasTranscription-BasedScaffolds
ofNucleolarStructureandFunction. . . . . . . . . . . . . . . . . . . . . . . . 551
AlexandriaJ.CockrellandJenniferL.Gerton
20 ATransientMystery:NucleolarChannelSystems. . . . . . . . . . . . . 581
ClaudiaC.Preston,AshleyC.Stoddard,andRandolphS.Faustino
PartV NuclearActinRoleinPolarization,GenomeOrganization,
andGeneExpression
21 CellularPolarityTransmissiontotheNucleus. . . . . . . . . . . . . . . . . 597
PaulinaNastałyandPaoloMaiuri
22 TheRoleofNuclearActininGenomeOrganizationandGene
ExpressionRegulationDuringDifferentiation. . . . . . . . . . . . . . . . . 607
SyedRazaMahmood,NadineHosnyElSaid,
andPiergiorgioPercipalle
23 NuclearActinDynamicsinGeneExpression,DNARepair,
andCancer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625
YuanjianHuang,ShengzheZhang,andJae-IlPark