Genome Organization and Function in the Cell Nucleus

By way of its clear and logical structure, as well as abundant highresolution illustrations, this is a systematic survey of the players and pathways that control genome function in the mammalian cell nucleus. As such, this handbook and reference ties together recently gainedknowledge from a variety of scientific disciplines and approaches, dissecting all major genomic events: transcription, replication, repair,recombination and chromosome segregation. A special emphasis is put on transcriptional control, including genome-wide interactions andnon-coding RNAs, chromatin structure, epigenetics and nuclear organization.With its focus on fundamental mechanisms and the associated biomolecules, this will remain essential reading for years to come.

List of contents

PrefaceDECIPHERING DNA SEQUENCE INFORMATIONIntroductionGenes and Transcribed RegionsNon-Coding Genomic ElementsRegulatory InformationIndividual Genetic Polymorphisms and Their Effect on Gene ExpressionConclusionDNA METHYLATIONIntroductionEukaryotic DNA MethyltransferasesDistribution of 5-Methylcytosine in the Mammalian GenomeControl of Gene Exression by DNA MethylationDNA DemethylationNUCLEOSOMES AS CONTROL ELEMENTS FOR ACCESSING THE GENOMEIntroduction and Basic TerminologyNucleosomes are the Building Blocks of ChromatinNucleosomes are Dynamic Macromolecular AssembliesHistone Variants and Their Effect on Nucleosome Structure and DynamicsHistone Modifications in Nucleosome and Chromatin StructureDNA Sequence and Nucleosome PositioningHistone Chaperones and Chromatin DynamicsOutlook and Concluding RemarksHISTONE MODIFICATIONS AND THEIR ROLE AS EPIGENETIC MARKSThe Complexity of Histone ModificationsRegulating Histone Modifications in ChromatinThe "Histone Code" HypothesisExploiting the Complexity of the Histone Code: "Crosstalk" Between Different ModificationsAre Histone Modifications Heritable Epigenetic Marks?ConclusionsCHROMATIN REMODELING AND NUCLEOSOME POSITIONINGIntroductionChromatin Remodeling ComplexesMechanisms of Nucleosome TranslocationsPositioning Nucleosomes in the GenomeGene Regulation via Nucleosome PositioningConclusionsTHE FOLDING OF THE NUCLEOSOME CHAINIntroductionExperimental SystemsNucleosome-Nucleosome InteractionsDNA Interactions with the Histone Octamer Protein CoreArchitectural Chromosomal Proteins and Chromatin StatesChromatin Fiber ConformationsConclusionsTHE CROWDED ENVIRONMENT OF THE GENOMEIntroductionBasicsPhysicochemical Parameters of the Genome's EnvironmentImplications of a Crowded Environment for the Conformation of the Interphase GenomeAssembly and Localization of Macromolecular Machines for Genome Transcription and ReplicationThe Environment of the Genome during MitosisEffects of a Crowded Environment on Searching for Targets in the GenomeThe Relative Importance of Entropic and Ionic Interactions for the Conformations and Interactions of Macromolecules in the NucleusThe Evolution of GenomesTHE NUCLEAR LAMINA AS A CHROMATIN ORGANIZERIntroductionGenome Organization with Respect to the Nuclear PeripheryInteractions between NE Proteins and Chromatin Proteins/Chromatin Regulatory ProteinsMechanisms Directing Changes in Genome Organization during DevelopmentGene Regulation as a Consequence of Peripheral PositioningPeripheral Chromatin Organization and DiseaseClosing RemarksTHREE-DIMENSIONAL ARCHITECTURE OF GENOMESIntroduction3C-Based Methods to Study Chromosome ArchitectureChromosome Architecture as Seen by 3C-Based Assays3C-Based Data and Single Cell ObservationsTowards an Integrated 3C-Based View of Genome ArchitectureTRANSCRIPTIONAL INITIATION: FREQUENCY, BURSTING, AND TRANSCRIPTION FACTORIESTranscription in Mammalian NucleiTranscription Is an Infrequent EventTranscription is NoisyWhat Causes "Bursting"?ConclusionPROCESSING OF mRNA AND QUALITY CONTROLIntroductionBiosynthesis of Messenger RNANuclear Quality ControlCytoplasmic Messenger RNA Quality Control: Nonsense-Mediated Decay, No-Go and Non-Stop DecayConcluding RemarksTHE NUCLEOLUSIntroductionThe Nucleolus and Its DNAThe Nucleolus and RNPs: Temporary Visitors or Permanent Residents? The Nucleolar ProteomeConcluding RemarksNON-CODING RNAs AS REGULATORS OF TRANSCRIPTION AND GENOME ORGANIZATIONIntroductionClassification of Non-Coding RNAsSmall Regulatory RNAs and Their Diverse Nuclear FunctionsncRNAs in Dosage CompensationDevelopmental Regulation of Hox Clusters by Cis- and Trans-Acting ncRNAsMechanisms of Transcriptional Regulation by Long ncRNAsConclusionsRNA NETWORKS AS DIGITAL CONTROL CIRCUITS OF NUCLEAR FUNCTIONSIntroductionThe Information Content of the GenomeThe Hidden Layer of Developmentally Expressed Non-Coding RNAsRNA Control of Nuclear FunctionsRNA as the Adaptor in Digital-Analog TransactionsRNA as the Substrate for Environment-Epigenome InteractionsConclusionDNA REPLICATION AND INHERITANCE OF EPIGENETIC STATESReplication in a Chromatin Context: Basic Issues and PrinciplesDuplication of Nucleosome OrganizationMaintenance of Epigenetic Marks and Post-Translational ModificationsConcluding RemarksINTERPLAY AND QUALITY CONTROL OF DNA DAMAGE REPAIR MECHANISMSIntroductionDNA Repair PathwaysRepairing DSBsRepair During ReplicationInterplay and Quality Control During DNA Damage RepairApplications of Mechanistic Insight in DNA Repair in Anti-Cancer TreatmentHIGHER ORDER CHROMATIN ORGANIZATION AND DYNAMICSIntroductionHigher Order Chromatin Organization: From 10-nm Thick Nucleosome Chains to Chromosome TerritoriesGenome AccessibilityMobility of Chromosomal Loci and Nuclear BodiesMitosis Causes Drastic Changes of Chromosome Territory Proximity Patterns in Cycling CellsLarge-Scale Chromatin Dynamics in Nuclei of Cycling and Post-Mitotic CellsConsiderations on Possible Mechanisms of Large-Scale Chromatin DynamicsTHE MITOTIC CHROMOSOME: STRUCTURE AND MECHANICSIntroductionStructural Components of Mitotic ChromosomesLarge-Scale Organization of Mitotic ChromosomesMechanics of Mitotic ChromosomesMolecular Connectivity of Mitotic ChromosomesA Model for Mitotic Chromosome Structure and FunctionOpen QuestionsMEIOTIC CHROMOSOME DYNAMICSIntroductionRecombination at the DNA LevelCoordination between Recombination and Chromosome DynamicsHomologous Chromosome PairingMeiotic Recombination as a Paradigm for Spatial Patterning along ChromosomesUNDERSTANDING GENOME FUNCTION: QUANTITATIVE MODELING OF CHROMATIN FOLDING AND CHROMATIN-ASSOCIATED PROCESSESModeling of Genome FunctioningLarge-Scale Chromatin FoldingAssembly of Chromatin-Associated Multiprotein ComplexesOutlook

About the author

Karsten Rippe leads the Research Group Genome Organization & Function at the German Cancer Research Center and the BioQuant Institute in Heidelberg, Germany. In his research, he combines molecular/cell biology and physics to quantitatively investigate and model the relation between nuclear DNA organization and cell function. Karsten Rippe has obtained his academic degrees from the University of
Göttingen while working at the Max Planck Institute for Biophysical Chemistry and continued his scientific career at the University of Oregon in Eugene and the Kirchhoff-Institut für Physik in Heidelberg. He has authored more than 80 scientific publications in the fields of DNA structure, transcription and chromatin and has received several scientific awards, including the Otto Hahn medal of the Max Planck Society and the European Beckman DNA Award.

Summary

By way of its clear and logical structure, as well as abundant highresolution illustrations, this is a systematic survey of the players and pathways that control genome function in the mammalian cell nucleus. As such, this handbook and reference ties together recently gained
knowledge from a variety of scientific disciplines and approaches, dissecting all major genomic events: transcription, replication, repair,
recombination and chromosome segregation. A special emphasis is put on transcriptional control, including genome-wide interactions and
non-coding RNAs, chromatin structure, epigenetics and nuclear organization.

With its focus on fundamental mechanisms and the associated biomolecules, this will remain essential reading for years to come.

Product details

• Authors: Karsten Rippe
• Assisted by: Karste Rippe (Editor), Karsten Rippe (Editor)
• Publisher: Wiley-VCH
• Languages: English
• Product format: Hardback
• Released: 01.11.2011
• EAN: 9783527326983
• ISBN: 978-3-527-32698-3
• No. of pages: 568
• Dimensions: 179 mm x 248 mm x 33 mm
• Weight: 1210 g
• Illustrations: 73 SW-Abb., 30 Farbabb., 9 Tabellen
• Subjects: Natural sciences, medicine, IT, technology > Biology > Genetics, genetic engineering; Chemie, Physik, Genetik, Biophysik, Molekularbiologie, Molekulargenetik, Life Sciences, genom, ZELLBIOLOGIE, Biowissenschaften, Chemische Biologie, chemistry, Physics, Biophysics, Cell Biology, Biochemie u. Chemische Biologie, Biochemistry (Chemical Biology), Molecular Genetics