Epigenetics And Chromatin,9783540233725

Epigenetics And Chromatin

by
ISBN13: 9783540233725
ISBN10: 3540233725
Format: Hardcover
Pub. Date: 2005-03-31
Publisher(s): Springer Nature
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Summary

Epigenetics refers to heritable patterns of gene expression which do not depend on alterations of genomic DNA sequence. This book provides a state-of-the-art account of a few selected hot spots by scientists at the edge in this extremely active field. It puts special emphasis on two main streams of research. One is the role of post-translational modifications of proteins, mostly histones, on chromatin structure and accessibility. The other one deals with parental genomic imprinting, a process which allows to express a few selected genes from only one of the parental allele while extinguishing the other.

Table of Contents

Chromatin Remodeling Factors and DNA Replication
1(30)
P. Varga-Weisz
Introduction
1(1)
Chromatin and Chromatin Remodeling Factors
2(3)
Chromatin
2(1)
Histone Modification Enzymes
3(1)
ATP-Dependent Chromatin Remodeling Factors
4(1)
Chromatin Structure and DNA Replication
5(2)
Chromatin Assembly
7(6)
Histone Chaperones
7(2)
Chromatin Assembly Factor 1, a Replication-Coupled Histone Chaperone
9(1)
CAF-1 Functions in the Inheritance of Chromatin States
9(1)
Histone Chaperone ASF1
10(1)
Histone Chaperones and Heterochromatin Replication
11(1)
Histone Variants
11(1)
DNA Replication-Independent Chromatin Assembly
12(1)
Histone Modifications and Chromatin Replication
13(1)
Histone Deacetylation During Chromatin Replication
13(1)
Histone Acetylation at the Replication Site
13(1)
ATP-Dependent Chromatin Remodeling Factors in Chromatin Replication
14(5)
ISWI Complexes in Chromatin Assembly in Vitro
14(3)
ISWI Complexes and Their Role in Chromatin Replication in Vivo
17(2)
The Assembly of Higher Order Chromatin Structures
19(1)
PCNA, a Central Coordinator of Epigenetic Inheritance
20(1)
Mechanisms of Epigenetic Inheritance Through Chromatin: Conclusion
21(10)
References
21(10)
Epigenetic Inheritance of Chromatin States Mediated by Polycomb and Trithorax Group Proteins in Drosophila
31(34)
J. Dejardin
G. Cavalli
Introduction
31(2)
Proteins of the Polycomb Group of Genes
33(13)
PcG Complexes
33(1)
The ESC-E(Z) Complex
33(2)
The Polycomb Repressive Complex 1
35(1)
Other Identified PcG Proteins and Partners
36(1)
Targeting of PcG-Mediated Repression
37(1)
PcG Response Elements
37(2)
Chromatin Determinants Associated with Targeting
39(4)
Mechanisms of Repression
43(1)
Spreading or Looping?
43(1)
Proposed Silencing Mechanisms
44(2)
Proteins of the Trithorax Group
46(8)
trxG Complexes
48(1)
The Trithorax Acetylation Complex (TAC1)
48(1)
The Brahma Complex
48(1)
The GAF--FACT Complex
49(1)
Other trxG Complexes and Partners
49(1)
Targeting of trxG Complexes at TREs
49(2)
Mechanisms of Action
51(3)
Modes of Inheritance
54(1)
Concluding Remarks
55(10)
References
56(9)
How to Pack the Genome for a Safe Trip
65(26)
C. Caron
J. Govin
S. Rousseaux
S. Khochbin
Introduction
65(2)
Synthesis of Histone Variants
67(4)
Non-Testis-Specific Core Histone Variants
68(1)
Testis-Specific Histone Variants
69(1)
Linker Histones
69(1)
Core Histones
70(1)
Histone Modifications
71(3)
Acetylation
72(1)
Ubiquitination
73(1)
Phosphorylation
73(1)
Methylation
74(1)
Transition Proteins
74(1)
Final Components of the Sperm Chromatin
75(2)
Protamines
76(1)
Histones
77(1)
Mechanisms Controlling Post-Meiotic Chromatin Reorganization: A General Discussion
77(5)
Active Transcription Followed by Repression in Round Spermatids
78(1)
Functional Link Between Histone Acetylation and Chromatin Condensation and Histone Replacement
79(1)
Does Histone Ubiquitination Play a Role in Spermatid-Specific Chromatin Remodeling?
80(1)
Is There a Spermiogenesis-Specific Histone Code?
81(1)
Do Histone Variants Play a Role in Spermatid-Specific Chromatin Remodeling?
82(1)
Concluding Remarks
82(9)
References
84(7)
Chromatin Modifications on the Inactive X Chromosome
91(32)
H.R. Cohen
M.E. Royce-Tolland
K.A. Worringer
B. Panning
Introduction
91(1)
Features of Xi Chromatin
92(9)
Histone H3 Lysine 9 Methylation
92(2)
Histone H3 Lysine 27 Methylation
94(1)
Methylation at Other Histone H3 Residues
95(1)
Histone Acetylation
96(1)
Histone MacroH2A
97(1)
Other Variant Histones
98(1)
Nucleosome Position
98(1)
Shape of the Xi
98(1)
DNA Methylation
99(1)
Late Replication Timing
100(1)
Xist RNA
101(1)
Redundant Mechanisms Maintain Silencing
101(1)
Chromatin at the Xic
101(2)
Histone Modifications
102(1)
DNA Methylation
102(1)
Replication Timing
103(1)
Genes that Escape X-Inactivation
103(2)
Histone Modifications
103(1)
DNA Methylation
104(1)
Replication Timing
104(1)
Chromosome Organization
104(1)
Developmental Regulation of X-Inactivation
105(6)
Three Stages of X-Inactivation
105(2)
Embryonic Stem Cells
107(1)
Extraembryonic Cells
108(1)
Reactivation of the Xi
109(2)
Chromatin Features of the X Chromosomes Prior to X-Inactivation
111(3)
Imprinted X-Inactivation
111(1)
Random X-Inactivation
112(2)
Conclusion
114(9)
References
115(8)
Chromatin Mechanisms in Drosophila Dosage Compensation
123(28)
M. Taipale
A. Akhtar
Introduction
123(1)
The MSL Complex
124(9)
MSL-1
126(1)
MSL-2
127(1)
MSL-3
127(1)
MOF
128(1)
MLE
129(2)
JIL-1
131(1)
roX1 and roX2
131(1)
roX Genes as Non-Coding RNAs
132(1)
roX Loci as Chromatin Entry Sites
132(1)
Targeting, Assembly and Spreading of the MSL Complex
133(3)
Targeting and Assembly
133(2)
Spreading
135(1)
Cracking the Code X
136(2)
Establishing the Code
136(1)
Reading the Code
137(1)
Molecular Mechanism of Dosage Compensation
138(3)
Initiation Versus Elongation
138(1)
The Inverse Effect Hypothesis
139(2)
The Origin and Evolution of the MSL Complex
141(10)
References
143(8)
DNA Methylation in Epigenetic Control of Gene Expression
151(18)
A. Razin
B. Kantor
Introduction
151(2)
Changes in Gene-Specific Methylation Patterns During Early Embryo Development
153(1)
Effect of Methylation on Gene Expression
154(5)
Direct Transcription Inhibition
154(2)
Indirect Transcription Inhibition
156(3)
DNA Methylation and Genomic Imprinting
159(3)
DNA Methylation and Disease
162(1)
Concluding Remarks
163(6)
References
163(6)
The Epigenetic Breakdown of Cancer Cells: From DNA Methylation to Histone Modifications
169(14)
E. Ballestar
M. Esteller
Introduction
169(2)
What Is Responsible for DNA Methylation and for How Deregulation Occurs?
171(2)
Is Methylation Specific to the Tumor Type?
173(1)
Connecting DNA Methylation Changes with Transcription: Chromatin Mechanisms
174(4)
Can We Reactivate Epigenetically Silenced Genes? Towards Epigenetic Therapy
178(5)
References
178(5)
Developmental Regulation of the β-Globin Gene Locus
183(24)
L. Chakalova
D. Carter
E. Debrand
B. Goyenechea
A. Horton
J. Miles
C. Osborne
P. Fraser
Introduction
183(1)
The β-Globin Clusters and Their Ontogeny
184(1)
Models for Studying the β-Globin Locus
185(1)
The LCR Is Required for High-Level Expression
186(2)
The Role of Individual HS
188(1)
Gene Competition and the LCR Holocomplex
189(1)
The β-Globin Locus Resides in a Region of Tissue-Specific Open Chromatin
190(1)
The Role of Insulators
191(1)
Intergenic Transcription
192(1)
Intergenic Promoters
193(1)
Histone Modification and Developmental Globin Gene Expression
194(1)
The Role of Intergenic Transcription
195(1)
The Cell Cycle Connection
196(1)
The Corfu Deletion
197(1)
Higher Order Folding and Long-Range Regulation
198(1)
Nuclear Organization
199(1)
Summary Model
200(7)
References
201(6)
Epigenetic Regulation of Mammalian Imprinted Genes: From Primary to Functional Imprints
207(30)
M. Weber
H. Hagege
N. Aptel
C. Brunel
G. Cathala
T. Forne
Introduction
207(1)
Imprinting Evolution
208(3)
Conservation of Parental Genomic Imprinting in Therian Mammals
208(1)
Theories on the Evolution of Parental Genomic Imprinting
209(1)
The Parental Conflict Theory
210(1)
Alternative Theories
211(1)
Characteristics of Mammalian Imprinted Genes
211(1)
Epigenetic Control of Imprinted Genes
212(4)
DNA Methylation
212(2)
Histone Modifications
214(1)
Asynchronous DNA Replication Timing
215(1)
Chromatin Architecture
216(1)
The Parental Genomic Imprinting Cycle
216(9)
Erasure
216(2)
Establishment
218(1)
Primary Imprinting Marks
218(1)
Imprinting Centres
219(2)
Maintenance
221(1)
Monoallelic Expression of Imprinted Genes
222(1)
Formatting for Gene Expression
223(1)
Acquisition of Functional Imprints
223(2)
Conclusion
225(12)
References
226(11)
Seed Development and Genomic Imprinting in Plants
237(26)
C. Kohler
U. Grossniklaus
Introduction
237(1)
Seed Development in Angiosperms
238(1)
Development and Function of the Endosperm
238(3)
A Role for Genomic Imprinting in Seed Development?
241(1)
The Discovery of Genomic Imprinting in Maize
242(1)
Studies on Other Potentially Imprinted Genes in Maize
243(1)
Maternal Control of Early Seed Development in Arabidopsis
244(2)
Intragenomic Parental Conflict and the Evolution of Genomic Imprinting
246(1)
Imprinting of the MEDEA Locus in Arabidopsis
247(2)
Function of MEDEA During Gametophyte and Seed Development
249(2)
Imprinting of the FWA Locus in the Female Gametophyte
251(1)
The Role of Imprinting During Gametophyte and Seed Development
252(1)
Imprinting and Apomixis
253(1)
Possible Epigenetic Marks Distinguishing Maternal and Paternal Alleles
254(3)
Chromatin Structure
254(1)
DNA Methylation During Gametogenesis
255(1)
DNA Methylation During Seed Development
256(1)
Conclusions
257(6)
References
257(6)
Subject Index 263

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