Keywords:
Mammals -- Genetics.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (596 pages)
Edition:
1st ed.
ISBN:
9783527640010
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=843677
DDC:
572.8619
Language:
English
Note:
Intro -- Genome Organization and Function in the Cell Nucleus -- Contents -- Preface -- List of Contributors -- 1: Deciphering DNA Sequence Information -- 1.1: Introduction -- 1.2: Genes and Transcribed Regions -- 1.2.1: Open Reading Frames -- 1.2.2: Mapping Transcriptional Start Sites -- 1.2.3: Mapping Untranslated Regions on mRNA -- 1.3: Non-Coding Genomic Elements -- 1.3.1: Pseudogenes -- 1.3.2: Repeats -- 1.3.3: Structural Variants -- 1.3.4: Methods for SV Detection -- 1.3.5: Transposons and Retrotransposons -- 1.4: Regulatory Information -- 1.4.1: Classes of Regulatory Elements -- 1.4.2: Transcription Factor Binding Motifs -- 1.4.3: Allele-Specific Expression -- 1.5: Individual Genetic Polymorphisms and Their Effect on Gene Expression -- 1.6: Conclusion -- 2: DNA Methylation -- 2.1: Introduction -- 2.1.1: Discovery of 5-Methylcytosine in DNA -- 2.1.2: Epigenetic Control of Gene Expression -- 2.2: Eukaryotic DNA Methyltransferases -- 2.2.1: Dnmt1 -- 2.2.2: The Dnmt3 Family -- 2.2.3: Cooperative Function of Dnmts -- 2.3: Distribution of 5-Methylcytosine in the Mammalian Genome -- 2.3.1: Spatial Distribution of 5-Methylcytosine -- 2.3.2: CpG Islands and Promoter Regulation -- 2.3.3: Repetitive DNA Sequences -- 2.3.4: Temporal Distribution of 5-Methylcytosine -- 2.4: Control of Gene Expression by DNA Methylation -- 2.4.1: Loss of Transcription Factor Binding -- 2.4.2: Methyl-CpG Binding Proteins -- 2.4.3: Interconnection of DNA Methylation with Other Epigenetic Pathways -- 2.4.4: DNA Methylation, Higher Order Chromatin Structure, and Nuclear Architecture -- 2.5: DNA Demethylation -- 3: Nucleosomes as Control Elements for Accessing the Genome -- 3.1: Introduction and Basic Terminology -- 3.2: Nucleosomes are the Building Blocks of Chromatin -- 3.2.1: Histones -- 3.2.2: Protein DNA Interactions in the Nucleosome.
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3.2.3: The Structure of Nucleosomal DNA -- 3.3: Nucleosomes Are Dynamic Macromolecular Assemblies -- 3.3.1: Mechanisms to Promote Histone Exchange In Vivo -- 3.3.2: In Vitro Determination of Nucleosome Stability -- 3.4: Histone Variants and Their Effect on Nucleosome Structure and Dynamics -- 3.4.1: Variant Nucleosome Structures -- 3.5: Histone Modifications in Nucleosome and Chromatin Structure -- 3.6: DNA Sequence and Nucleosome Positioning -- 3.6.1: Mechanisms for Nucleosome Exclusion -- 3.6.2: Features that Promote Nucleosome Formation -- 3.7: Histone Chaperones and Chromatin Dynamics -- 3.7.1: Transcription -- 3.7.2: DNA Replication -- 3.7.3: DNA Repair -- 3.7.4: Mechanism of Chaperone-Mediated Nucleosome Assembly and Disassembly -- 3.8: Outlook and Concluding Remarks -- 4: Histone Modifications and Their Role as Epigenetic Marks -- 4.1: The Complexity of Histone Modifications -- 4.2: Regulating Histone Modifications in Chromatin -- 4.3: The "Histone Code" Hypothesis -- 4.3.1: Defining Histone "Marks." Why Is Histone Modification so Complex? -- 4.3.2: Recognizing Histone Modifications: "Reader" Domains -- 4.4: Exploiting the Complexity of the Histone Code: "Crosstalk" Between Different Modifications -- 4.4.1: Histone "Crosstalk": Increased Code Complexity and Signal Integration -- 4.4.2: Histone Crosstalk: Sequential Processes on Chromatin -- 4.5: Are Histone Modifications Heritable Epigenetic Marks? -- 4.6: Conclusions -- 5: Chromatin Remodeling and Nucleosome Positioning -- 5.1: Introduction -- 5.2: Chromatin Remodeling Complexes -- 5.2.1: ATPase Families -- 5.2.2: Accessory Subunits of Chromatin Remodeling Complexes -- 5.2.3: Activities of Chromatin Remodeling Factors -- 5.3: Mechanisms of Nucleosome Translocations -- 5.3.1: The Loop-Recapture Mechanism for Nucleosome Translocation.
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5.3.2: Mechanisms for Targeting Nucleosomes to Certain Site -- 5.4: Positioning Nucleosomes in the Genome -- 5.4.1: DNA Sequence-Dependent Binding Affinities of the Histone Octamer -- 5.4.2: Genome-Wide Analysis of Nucleosome Positions -- 5.4.3: Nucleosome Positions at Promoters and Enhancers -- 5.4.4: Prediction of Nucleosome Positions from the DNA Sequence -- 5.4.5: Effects of Chromatin Remodelers on Nucleosome Positioning -- 5.5: Gene Regulation via Nucleosome Positioning -- 5.5.1: Competitive Binding of Transcription Factors and Nucleosomes -- 5.5.2: Remodeler and Nucleosomes as Molecular Switches -- 5.6: Conclusions -- 6: The Folding of the Nucleosome Chain -- 6.1: Introduction -- 6.2: Experimental Systems -- 6.2.1: Native Chromatin Fragments -- 6.2.2: Reconstituted Nucleosome Chains -- 6.3: Nucleosome-Nucleosome Interactions -- 6.3.1: The Strength of Nucleosome-Nucleosome Interactions -- 6.3.2: Interactions of the Globular Part of the Histone Octamer Core -- 6.3.3: Contributions of Histone Tails to Nucleosome-Nucleosome Interactions -- 6.4: DNA Interactions with the Histone Octamer Protein Core -- 6.5: Architectural Chromosomal Proteins and Chromatin States -- 6.5.1: Linker Histones -- 6.5.2: Other Architectural Chromosomal Proteins -- 6.5.3: Chromatin States -- 6.6: Chromatin Fiber Conformations -- 6.6.1: Solenoid Chromatin Fiber Models -- 6.6.2: Chromatin Fibers with Crossed Linker DNA -- 6.7: Conclusions -- 7: The Crowded Environment of the Genome -- 7.1: Introduction -- 7.2: Basics -- 7.2.1: Macromolecular Crowding -- 7.2.2: Depletion or Entropic Forces -- 7.2.3: Phase Separation -- 7.3: Physicochemical Parameters of the Genome's Environment -- 7.3.1: The Ionic Environment(s) -- 7.3.2: The Macromolecular Environment -- 7.4: Implications of a Crowded Environment for the Conformation of the Interphase Genome.
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7.4.1: Chromosomes as Polyelectrolyte Polymers -- 7.4.2: Formation of Loops in Polynucleosome Chains -- 7.4.3: Chromosomes and the Interchromatin Compartment Viewed as Separate Phases -- 7.5: Assembly and Localization of Macromolecular Machines for Genome Transcription and Replication -- 7.5.1: Entropic Forces in the Assembly of Transcription Factories -- 7.5.2: Localization of Transcription and Replication Factories on the Surface of Chromosome Territories -- 7.6: The Environment of the Genome during Mitosis -- 7.7: Effects of a Crowded Environment on Searching for Targets in the Genome -- 7.7.1: The Advantage of Anomalous Diffusion -- 7.7.2: Finding Targets in the Genome -- 7.8: The Relative Importance of Entropic and Ionic Interactions for the Conformations and Interactions of Macromolecules in the Nucleus -- 7.9: The Evolution of Genomes -- 8: The Nuclear Lamina as a Chromatin Organizer -- 8.1: Introduction -- 8.2: Genome Organization with Respect to the Nuclear Periphery -- 8.2.1: Chromosome and Gene Positioning -- 8.2.2: Epigenetic Marks -- 8.2.3: A Distinct Microenvironment at the NPC -- 8.3: Interactions between NE Proteins and Chromatin Proteins/Chromatin Regulatory Proteins -- 8.3.1: Interactions with Chromatin and DNA -- 8.3.2: Epigenetically Marked Chromatin Interactions -- 8.3.3: Chromatin-Modifying Enzymes -- 8.4: Mechanisms Directing Changes in Genome Organization during Development -- 8.4.1: Dynamic Changes in Genome Organization in Development -- 8.4.2: An Affinity Mechanism for Directing Genes to the Periphery -- 8.4.3: Correlations between Gene Movement and Repression/Activation -- 8.5: Gene Regulation as a Consequence of Peripheral Positioning -- 8.5.1: General Silencing from the Peripheral Environment -- 8.5.2: Directed Gene Silencing from NE Proteins -- 8.5.3: Gene Activation from the NE.
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8.6: Peripheral Chromatin Organization and Disease -- 8.6.1: NE-Linked Diseases -- 8.6.2: Changes in Heterochromatin Organization in Disease -- 8.7: Closing Remarks -- 9: Three-Dimensional Architecture of Genomes -- 9.1: Introduction -- 9.2: 3C-Based Methods to Study Chromosome Architecture -- 9.2.1: Chromosome Conformation Capture -- 9.2.2: 4C: 3C on Chip, or Circular 3C -- 9.2.3: 5C: 3C Carbon Copy -- 9.2.4: Chip-loop and Chia-PET -- 9.2.5: Hi-C -- 9.2.6: Comparison of 3C-Based Methods, Strengths, and Weaknesses -- 9.3: Chromosome Architecture as Seen by 3C-Based Assays -- 9.3.1: Formation of Chromatin Loops -- 9.3.1.1: Cis Interactions: Chromatin Loops in the Beta-Globin Locus -- 9.3.1.2: Trans Interactions: Associations Between the X Chromosome Inactivation Centers -- 9.3.2: Gene Associations in Cis and in Trans -- 9.3.3: Chromosome Compartmentalization -- 9.3.4: Chromosome Territories and Nuclear Organization -- 9.3.5: Polymer Aspects of Chromosome Architecture -- 9.4: 3C-Based Data and Single Cell Observations -- 9.5: Towards an Integrated 3C-Based View of Genome Architecture -- 10: Transcriptional Initiation: Frequency, Bursting, and Transcription Factories -- 10.1: Transcription in Mammalian Nuclei -- 10.1.1: General Introduction -- 10.2: Transcription Is an Infrequent Event -- 10.3: Transcription Is Noisy -- 10.3.1: Extrinsic and Intrinsic Noise -- 10.3.2: Studies of Noise Suggest Transcription Occurs in "Bursts -- 10.3.3: Visualizing Bursts of Transcription in Real Time -- 10.4: What Causes "Bursting"? -- 10.4.1: How Long Does a Burst Last? -- 10.4.2: Typical Transcription Factors Do Not Bind Long Enough to Account for Bursting -- 10.4.3: Effects of Chromatin Remodeling and Histone Modifications on Transcription Bursts -- 10.4.4: Transcription Factories -- 10.5: Conclusion -- 11: Processing of mRNA and Quality Control -- 11.1: Introduction.
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11.2: Biosynthesis of Messenger RNA.
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