The Histone Code and Beyond

by Berger, S. L.; Nakanishi, O.; Haendler, B.

• ISBN13: 9783540278573
• ISBN10: 3540278575
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-04-11
• Publisher: Springer Verlag

Summary

Methylation of DNA at cytosine residues as well as post-translational modifications of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contribute to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. The use of a combination of biochemical, genetic and structural approaches has allowed demonstration of the role of chromatin structure in transcriptional control. The structure of nucleosomes has been elucidated and enzymes involved in DNA or histone modifications have been extensively characterized. Since deregulation of epigenetic marks has been reported in many cancers, a better understanding of the underlying molecular mechanisms bears the promise that new drug targets may soon be found. The newest developments in this quickly developing field are presented in this book.

Table of Contents

1 The Role of Histone Modifications in Epigenetic Transitions During Normal and Perturbed Development
S. Kubicek, G. Schotta, M. Lachner, R. Sengupta, A. Kohlmaier, L. Perez-Burgos, Y. Linderson, J.H.A. Martens, R.J. O'Sullivan, B.D. Fodor, M. Yonezawa, A.H.EM. Peters, T. Jenuwein	1	(28)
1.1 The Distinction Between Genome and Epigenomes	2	(3)
1.2 Activating Histone Modifications	5	(3)
1.3 Repressive Histone Modifications	8	(2)
1.4 Reprogramming of Epigenetic Modifications	10	(2)
1.5 Persistence of Soma-Specific Epigenetic Marks in Cloned Embryos	12	(3)
1.6 Epigenetic Transitions During Tumorigenesis	15	(2)
1.7 From Basic to Applied Research	17	(4)
References	21	(8)
2 Nucleosome Structure and Function
J.V. Chodaparambil, R.S. Edayathumangalam, Y. Bao, Y.-J. Park, K. Luger	29	(18)
2.1 Introduction	30	(1)
2.2 Nucleosome Structure	30	(6)
2.2.1 Histone Fold	30	(1)
2.2.2 Histone Fold Extensions	31	(1)
2.2.3 Histone Tails	32	(2)
2.2.4 DNA Structure	34	(1)
2.2.5 Higher-Order Structures	35	(1)
2.3 Nucleosome Dynamics	36	(6)
2.3.1 DNA "Breathing"	37	(2)
2.3.2 Histone Dimer Removal and Exchange	39	(2)
2.3.3 Complete Histone Removal	41	(1)
2.4 Summary and Outlook	42	(1)
References	42	(5)
3 The Role of Snf2-Related Proteins in Cancer
T. Owen-Hughes	47	(14)
3.1 Introduction	47	(2)
3.2 The SNF2 Subfamily	49	(2)
3.3 Mi2/CHD3/4 Subfamily	51	(1)
3.4 The ISWI Subfamily	52	(1)
3.5 The LSH Subfamily	52	(1)
3.6 Conclusions	53	(1)
References	53	(8)
4 Imitation Switch Complexes
J. Mellor	61	(28)
4.1 Introduction	62	(1)
4.2 The ISWI Proteins	63	(1)
4.2.1 ISWI ATPases Contain Distinct Structural Motifs	63	(1)
4.2.2 Related ISWI ATPases in Eukaryotes	64	(1)
4.3 ISWI Complexes	64	(12)
4.3.1 ACF and Related Complexes: CHRAC, WSTF and NoRC	70	(3)
4.3.2 Yeast Iswl a	73	(1)
4.3.3 NURF and Related Complexes	73	(1)
4.3.4 Yeast Iswlb	74	(1)
4.3.5 SNF2h-Cohesin	74	(2)
4.4 Roles for ISWI Complexes in Development, Differentiation and Disease	76	(4)
4.4.1 CERF	76	(1)
4.4.2 hNURF	76	(2)
4.4.3 DmNURF	78	(1)
4.4.4 WSTF and WCRF	79	(1)
4.5 ISWI Complexes and the Histone Code	80	(2)
References	82	(7)
5 How Is Epigenetic Information on Chromatin Inherited After DNA Replication?
Y. Nakatani, H. Tagami, E. Shestakova	89	(8)
5.1 Epigenetic Information on Chromatin	90	(1)
5.2 Nonconservative Nucleosome Segregation Model	91	(1)
5.3 Semiconservative Nucleosome Segregation Model	91	(4)
References	95	(2)
6 Polycomb Silencing Mechanisms and Genomic Programming
V. Pirrotta	97	(18)
6.1 Introduction	98	(1)
6.2 The Homeotic Paradigm	98	(1)
6.3 The Polycomb Group Proteins	99	(1)
6.4 Polycomb Response Elements	100	(1)
6.5 PRE Properties	101	(1)
6.6 Chromatin Modifications	102	(2)
6.7 Histone Methylation and Recruitment	104	(1)
6.8 The Silencing Mechanism	105	(1)
6.9 Alternative Modes of Action	106	(2)
6.10 Reprogramming	108	(1)
6.11 Export of PcG Proteins	109	(1)
References	110	(5)
7 CpG Island Methylation and Histone Modifications: Biology and Clinical Significance
M. Esteller	115	(12)
7.1 Introduction	116	(1)
7.2 Histone Modification Directs Chromatin Structure and Function	116	(2)
7.3 Alteration of the Histone Modification Patterns in Cancer Cells	118	(2)
7.4 Histone Deacetylase Inhibitors as Epigenetic Anticancer Drugs	120	(5)
References	125	(2)
8 Hi stone Post-Translational Modifications Regulate Transcription and Silent Chromatin in Saccharomyces cerevisiae
N.C. Tolga Emre, S.L. Berger	127	(28)
8.1 Introduction	128	(6)
8.1.1 Major Covalent Modifications of Histones: A Brief Overview	129	(3)
8.1.2 Cross-talk Among Histone Modifications and Their Functional Correlates	132	(2)
8.2 Histone H3 Ser10 Phosphorylation and Acetylation Regulate TATA Binding Protein Association During Transcriptional Initiation . . .	134	(2)
8.3 Histone H2B Ubiquitylation and Deubiquitylation Regulate Histone H3 Methylation During Transcription	136	(3)
8.4 Histone H2B Deubiquitylation Regulates Heterochromatic Silencing	139	(6)
8.4.1 Silent Chromatin in Budding Yeast	139	(3)
8.4.2 Ubiquitin Protease Ubp10 Regulates Silencing Through Histone H2B Deubiquitylation	142	(3)
8.5 Conclusions and Perspectives	145	(1)
References	146	(9)
9 Histone Acetylation-Mediated Chromatin Compaction During Mouse Spermatogenesis
J. Govin, C. Lestrat, C. Caron, C. Pivot-Pajot, S. Rousseaux, S. Khochbin	155	(18)
9.1 Introduction	156	(2)
9.2 Results	158	(5)
9.2.1 Induced Histone Acetylation in Postmeiotic Spermatogenic Cells	158	(1)
9.2.2 Brdt, a Unique Factor Capable of Specifically Inducing the Compaction of Acetylated Chromatin	159	(3)
9.2.3 Brdt Accumulation During Mouse Spermatogenesis	162	(1)
9.3 Discussion	163	(4)
9.4 Material and Methods	167	(2)
9.4.1 Spermatogenic Cell Fractionation	167	(1)
9.4.2 Cell Lines, Transfection and Cell Treatment	167	(1)
9.4.3 Immunofluorescence	167	(1)
9.4.4 Microscopy	168	(1)
9.4.5 In Vivo Cell Imaging	169	(1)
9.4.6 Western Blots	169	(1)
References	169	(4)
10 Role of Ubiquitin-Like Proteins in Transcriptional Regulation
R.T. Hay	173	(20)
10.1 The Family of Small Ubiquitin-Like Modifiers	174	(3)
10.2 SUMO-1 Modification and Transcription	177	(3)
10.3 NEDD8 Modification and Transcription	180	(1)
10.4 Transcriptional Control by Ubl-Specific Proteases	180	(2)
10.5 How Do Ubls Alter Transcription?	182	(2)
10.6 Models for Ubl Action	184	(3)
References	187	(6)
11 Interplay of the SUMO and MAP Kinase Pathways
S.-H. Yang, A.D. Sharrocks	193	(18)
11.1 Introduction	194	(1)
11.2 The SUMO Pathway	194	(1)
11.3 Specificity and Regulation of Sumoylation	195	(2)
11.4 Elk-1, MAP Kinase Pathways and Regulated Sumoylation	197	(2)
11.5 Cross-talk Between Sumoylation and Histone Deacetylases	199	(2)
11.6 SUMO E3 Ligases	201	(2)
11.7 Signalling to PIAS Proteins	203	(1)
11.8 Discussion and Perspectives	204	(2)
References	206	(5)
Previous Volumes Published in This Series	211