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Autor: Karsten Rippe
ISBN-13: 9783527640003
Einband: E-Book
Seiten: 594
Sprache: Englisch
eBook Typ: Adobe Digital Editions
eBook Format: E-Book
Kopierschutz: Adobe DRM [Hard-DRM]
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Genome Organization And Function In The Cell Nucleus

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1
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 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.
4
Preface

DECIPHERING DNA SEQUENCE INFORMATION
Introduction
Genes and Transcribed Regions
Non-Coding Genomic Elements
Regulatory Information
Individual Genetic Polymorphisms and Their Effect on Gene Expression
Conclusion

DNA METHYLATION
Introduction
Eukaryotic DNA Methyltransferases
Distribution of 5-Methylcytosine in the Mammalian Genome
Control of Gene Exression by DNA Methylation
DNA Demethylation

NUCLEOSOMES AS CONTROL ELEMENTS FOR ACCESSING THE GENOME
Introduction and Basic Terminology
Nucleosomes are the Building Blocks of Chromatin
Nucleosomes are Dynamic Macromolecular Assemblies
Histone Variants and Their Effect on Nucleosome Structure and Dynamics
Histone Modifications in Nucleosome and Chromatin Structure
DNA Sequence and Nucleosome Positioning
Histone Chaperones and Chromatin Dynamics
Outlook and Concluding Remarks

HISTONE MODIFICATIONS AND THEIR ROLE AS EPIGENETIC MARKS
The Complexity of Histone Modifications
Regulating Histone Modifications in Chromatin
The "Histone Code" Hypothesis
Exploiting the Complexity of the Histone Code: "Crosstalk" Between Different Modifications
Are Histone Modifications Heritable Epigenetic Marks?
Conclusions

CHROMATIN REMODELING AND NUCLEOSOME POSITIONING
Introduction
Chromatin Remodeling Complexes
Mechanisms of Nucleosome Translocations
Positioning Nucleosomes in the Genome
Gene Regulation via Nucleosome Positioning
Conclusions

THE FOLDING OF THE NUCLEOSOME CHAIN
Introduction
Experimental Systems
Nucleosome-Nucleosome Interactions
DNA Interactions with the Histone Octamer Protein Core
Architectural Chromosomal Proteins and Chromatin States
Chromatin Fiber Conformations
Conclusions

THE CROWDED ENVIRONMENT OF THE GENOME
Introduction
Basics
Physicochemical Parameters of the Genome's Environment
Implications of a Crowded Environment for the Conformation of the Interphase Genome
Assembly and Localization of Macromolecular Machines for Genome Transcription and Replication
The Environment of the Genome during Mitosis
Effects of a Crowded Environment on Searching for Targets in the Genome
The Relative Importance of Entropic and Ionic Interactions for the Conformations and Interactions of Macromolecules in the Nucleus
The Evolution of Genomes

THE NUCLEAR LAMINA AS A CHROMATIN ORGANIZER
Introduction
Genome Organization with Respect to the Nuclear Periphery
Interactions between NE Proteins and Chromatin Proteins/Chromatin Regulatory Proteins
Mechanisms Directing Changes in Genome Organization during Development
Gene Regulation as a Consequence of Peripheral Positioning
Peripheral Chromatin Organization and Disease
Closing Remarks

THREE-DIMENSIONAL ARCHITECTURE OF GENOMES
Introduction
3C-Based Methods to Study Chromosome Architecture
Chromosome Architecture as Seen by 3C-Based Assays
3C-Based Data and Single Cell Observations
Towards an Integrated 3C-Based View of Genome Architecture

TRANSCRIPTIONAL INITIATION: FREQUENCY, BURSTING, AND TRANSCRIPTION FACTORIES
Transcription in Mammalian Nuclei
Transcription Is an Infrequent Event
Transcription is Noisy
What Causes "Bursting"?
Conclusion

PROCESSING OF mRNA AND QUALITY CONTROL
Introduction
Biosynthesis of Messenger RNA
Nuclear Quality Control
Cytoplasmic Messenger RNA Quality Control: Nonsense-Mediated Decay, No-Go and Non-Stop Decay
Concluding Remarks

THE NUCLEOLUS
Introduction
The Nucleolus and Its DNA
The Nucleolus and RNPs: Temporary Visitors or Permanent Residents?
The Nucleolar Proteome
Concluding Remarks

NON-CODING RNAs AS REGULATORS OF TRANSCRIPTION AND GENOME ORGANIZATION
Introduction
Classification of Non-Coding RNAs
Small Regulatory RNAs and Their Diverse Nuclear Functions
ncRNAs in Dosage Compensation
Developmental Regulation of Hox Clusters by Cis- and Trans-Acting ncRNAs
Mechanisms of Transcriptional Regulation by Long ncRNAs
Conclusions

RNA NETWORKS AS DIGITAL CONTROL CIRCUITS OF NUCLEAR FUNCTIONS
Introduction
The Information Content of the Genome
The Hidden Layer of Developmentally Expressed Non-Coding RNAs
RNA Control
3
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.
Editiert von: Karsten Rippe
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 Gottingen 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 fur 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.

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Autor: Karsten Rippe
ISBN-13:: 9783527640003
ISBN: 3527640002
Verlag: Wiley-VCH
Seiten: 594
Sprache: Englisch
Auflage 1. Auflage
Sonstiges: Ebook