Genome Organization and Function in the Cell Nucleus

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