Chromatin structure and dynamics: state-of-the-art
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier
2004
|
| Edition: | 1. ed. |
| Series: | New comprehensive biochemistry
39 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXV, 507 S. Ill., graph. Darst. |
| ISBN: | 9780444515940 0444515941 044451595X |
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| adam_text | Contents
Preface vii
List of Contributors ix
Other Volumes in the Series xxiii
Chapter 1. Chromatin structure and dynamics: a historical perspective
E. Morton Bradbury and K.E. van Holds 1
1. Introduction 1
2. Advances in selected areas of chromatin research 1
2.1. Nucleosomes 1
2.1.1. The core particle 1
2.1.2. The chromatosome, and the role of the lysine rich
histones 2
2.1.3. Nucleosome assembly 3
2.2. Higher order chromatin structure 3
2.3. Histones 4
2.3.1. Histone sequences and variants 4
2.3.2. Histone modifications 6
2.3.3. Histone histone interactions 6
2.4. Chromatin and transcription 7
3. Conclusions and overview 8
References 9
Chapter 2. The core particle of the nucleosome
Joel M. Harp, B. Leif Hanson and Gerard J. Buniek 13
1. Introduction 13
2. Toward higher resolution nucleosome structure 16
3. Units of nucleosome structure 20
4. Structure of the core histones 22
5. DNA structure 25
6. DNA histone binding 29
7. Surface features of the NCP 30
8. Translation, libration, and screw axis motions of NCP elements .... 34
9. Crystal packing features of NCP and implications for higher
order chromatin structure 39
References 43
xiv
Chapter 3. Paradox lost: nucleosome structure and dynamics by the
DNA minicircle approach
Ariel Prunell and Andrei Sivolob 45
1. Introduction: the linking number paradox and DNA local
helical periodicity on the histone surface 45
2. Early topological studies: a single nucleosome on a
DNA minicircle 48
3. Polymerase induced positive supercoiling and linker positive
crossing in nucleosomes 52
4. A nucleosome on an homologous series of DNA minicircles:
a dynamic equilibrium between three distinct DNA
conformational states 53
4.1. Qualitative analysis 53
4.2. Quantitative analysis 56
4.2.1. Topology: general equations 56
4.2.2. Energetics 56
4.2.3. Loop most probable conformations and elastic
supercoiling free energies 58
4.3. DNA sequence dependent nucleosome structural and
dynamic polymorphism. A role for H2B N terminal
tail proximal domain 62
5. Nucleosomes in chromatin: a dynamic equilibrium 63
5.1. A displaceable equilibrium 63
5.1.1. Supercoiling constraints 63
5.1.2. Histone acetylation. Toward an invariant of chromatin
dynamics: the ALk per nucleosome parameter 64
5.2. Superstructural context of nucleosome dynamics in
chromatin 65
5.3. Topology and dynamics of linker histone containing
nucleosomes in chromatin 66
6. Conclusions 67
Acknowledgement 68
References 68
Chapter 4. The linker histones
A. Jerzmanowski 75
1. Introduction 75
2. Core and linker histones: a common name for different
proteins 75
3. Linker histones and chromatin structure 77
3.1. Mode of binding and location of histone HI in the
nucleosome 77
3.2. Linker histones and higher order chromatin structures 81
3.3. Dynamic character of HI binding to chromatin 83
XV
4. Variability of linker histones 85
4.1. Evolutionary perspective 85
4.2. Biological significance of HI diversity—evidence from
biochemical and molecular studies 90
5. Functional analysis of the role of linker histones in cells and organisms . . 91
5.1. Function of linker histones in simple eukaryotes 92
5.2. Function of linker histones in complex multicellular eukaryotes . 93
5.2.1. Experiments employing cell lines 93
5.2.2. Experiments employing whole organisms 94
6. Conclusions and perspectives 96
Acknowledgements 98
References 98
Chapter 5. Chromosomal HMG box proteins
Andrew A. Travers and Jean O. Thomas 103
1. Introduction 103
2. Structure and DNA binding 104
2.1. The HMG box domain 104
2.2. DNA binding 105
2.2.1. Structural basis for DNA binding and bending 105
2.2.2. Binding to distorted DNA structures 107
2.2.3. Role of the basic region in DNA binding 109
2.2.4. Role of the acidic region Ill
2.2.5. Structural basis for non sequence specific DNA
recognition 112
3. HMGB function 112
3.1. DNA bending as a major feature 112
3.2. HMGB proteins and chromatin structure 113
3.3. Nucleosome assembly and remodeling 115
3.4. HMGB proteins and transcription 118
3.4.1. Effects at the level of chromatin 118
3.4.2. Interactions with transcription factors 119
3.5. HMGB proteins and DNA repair 123
3.6. Post translational modifications of HMGB proteins 123
4. Other functions for HMGB proteins 124
Acknowledgements 125
References 125
Chapter 6. The role of HMGN proteins in chromatin function
Katherine L. West and Michael Bitstin 135
1. Introduction 135
2. Members of the HMGN family 135
2.1. Conservation between HMGN family members 136
2.2. Genomic organization of HMGN family members 136
xvi
3. Interaction of HMGN proteins with the nucleosome core particle ... 138
4. Interaction of HMGN proteins with nucleosome arrays 141
5. Post transcriptional modification of HMGN proteins 142
5.1. Phosphorylation 142
5.2. Acetylation 143
6. Activation of transcription by HMGN proteins in vitro 144
7. Models for chromatin unfolding by HMGN proteins 145
7.1. Interaction with core histone tails 145
7.2. Counteracting linker histone compaction 145
8. Association of HMGN proteins with transcription in vivo 146
9. Tissue specific expression of HMGN family members in vivo 148
10. Role of HMGN proteins in vivo 149
11. Conclusions 150
Abbreviations 151
References 151
Chapter 7. HMGA proteins: multifaceted players in nuclear function
Raymond Reeves and Dale Edberg 155
1. Introduction 155
2. Biological functions of HMGA proteins 155
3. HMGA proteins: flexible players in a structured world 157
4. HMGA biochemical modifications: a labile regulatory code 160
5. HMGA proteins, AT hooks and chromatin remodeling 166
6. HMGA proteins as potential drug targets 170
6.1. Methods to lower the cellular concentrations of
HMGA proteins 170
6.2. Drugs that non specifically compete with AT hooks peptides
for DNA binding 171
6.3. Drugs that block binding of HMGA proteins to specific
gene promoters 172
6.4. Drugs that specifically inactivate or cross link HMGA
proteins in vivo 173
7. Conclusions 175
Abbreviations 176
References 177
Chapter 8. Core histone variants
John R. Pehrson 181
1. CENP A 181
1.1. Sequence comparisons 182
1.2. Nucleosomes 183
1.3. Centromeric localization 183
1.4. Function 184
xvii
2. H2A.Z 185
2.1. Nucleosomes 186
2.2. Function 186
3. H2A.X 188
3.1. DNA double strand breaks and H2A.X phosphorylation 188
3.2. Function 189
4. MacroH2A 190
4.1. Sequence comparisons 190
4.2. Nucleosomes 191
4.3. Localization 192
4.4. Function 193
5. H3 replacement variants 193
5.1. Sequences 193
5.2. Localization 193
5.3. Function 194
5.4. Other H3 replacement variants 195
6. H2A.Bbd 195
7. Spermatogenesis 195
8. Cleavage stage variants 196
9. Concluding remarks 197
References 197
Chapter 9. Histone modifications
James R. Davie 205
1. Introduction 205
2. Histone phosphorylation 205
2.1. Histone phosphorylation and mitosis 207
2.2. Histone HI phosphorylation. transcription, and signal
transduction 209
2.3. H3 phosphorylation and transcriptional regulation 211
2.4. H3 kinases and phosphatase 212
2.5. Histone H3 phosphorylation and acetylation 213
2.6. Histone H2AX phosphorylation and DNA damage 214
2.7. N phosphorylation 216
3. Histone methylation 217
3.1. Histone methylation. gene regulation, and heterochromatin .... 218
3.2. Histone methyltransferases 221
3.2.1. H3 Lys 9 methyltransferases 222
3.2.2. H3 Lys 4 methyltransferases 223
3.2.3. H3 Lys 27 methyltransferases 224
3.2.4. H3 Lys 36 methyltransferases 224
3.2.5. H3 Lys 79 methyltransferases 224
3.2.6. H3 Arg methyltransferases 225
3.2.7. H4 Lys 20 methyltransferase 225
xviii
3.2.8. H4 Arg 3 methyltransferase 225
3.2.9. Ashl, a multi site histone methyltransferase 225
3.3. Histone methyltransferases, HATs, HDACs, and DNA
methyltransferases 225
4. Histone ubiquitination 227
5. Histone ubiquitination and histone methylation—trans histone
regulatory pathway 229
6. Histone ADP ribosylation 230
References 231
Chapter 10. The role of histone variability in chromatin
stability and folding
Juan Ausio and D. Wade Abbott 241
1. Introduction 241
2. Brief introduction to histone variants 242
2.1. Histone H2AX 242
2.2. Histone H2A.Z 245
2.3. MacroH2A 245
2.4. H2A Bbd 246
2.5. Centromeric variants 247
2.6. Histone HI micro and macroheterogeneity 248
3. Brief introduction to post translational
modifications 249
3.1. Histone acetylation 252
3.2. Histone phosphorylation 254
3.3. Histone methylation 255
3.4. Histone ubiquitination 257
3.5. Histone polyADP ribosylation 258
4. Brief introduction to DNA methylation 259
5. Chromatin folding and dynamics 260
5.1. Nucleosome stability 261
5.1.1. The role of DNA 264
5.1.2. The role of histones 266
5.2. Chromatin fiber folding 267
6. Histone variation and chromatin stability. A few
selected examples 269
6.1. Histone H2A.Z 270
6.2. Histone acetylation 272
6.2.1. The structure of the acetylated nucleosome
core particle 272
6.2.2. Is the acetylated chromatin fiber unfolded? 275
6.3. Histone H2A ubiquitination 275
7. Concluding remarks 279
References 279
xix
Chapter 11. Nucleosome modifications and their interactions; searching
for a histone code
Bryan M. Turner 291
1. The importance of residue specific modifications 292
2. Dynamics of histone modification 294
3. Modifications interact in cis 295
4. Modifications interact in trans 296
5. Interplay between histone modifications and DNA methylation 298
6. Short term changes; transcription initiation 299
7. Long term effects 300
8. A molecular memory mechanism 301
9. What should we expect of a histone code? 302
References 304
Chapter 12. DNA methylation and chromatin structure
Jordanka Zlatanova, Irina Stancheva and Paola Caiafa 309
1. Introduction 309
2. DNA methylation: the biology 311
2.1. The distribution of methylated CpGs in the genome is
not random 311
2.2. The enzymatic machinery involved in governing the DNA
methylation status 317
2.3. Methyl CpG binding proteins 319
2.4. DNA methylation and human disease 322
3. DNA methylation and transcriptional regulation: the
phenomenology 322
4. DNA methylation, insulators, and boundaries of chromatin
domains 325
5. Chromatin and DNA methylation 327
5.1. The histone acetylation link 327
5.2. The histone methylation link 330
5.3. The poly(ADP ribosyl)ation link 332
5.4. DNA methylation and chromatin structure: beyond the
post synthetic modifications of histones and other proteins .... 333
6. Concluding remarks 335
Acknowledgements 336
References 336
Chapter 13. Chromatin structure and function: lessons from imaging
techniques
David P. Bazett Jones and Christopher H. Eskiw 343
1. Introduction 343
2. Microscopy: a complementary approach 343
XX
2.1. Microscopical approaches 344
2.1.1. Transmission electron microscopy (TEM) 344
2.1.2. Scanning force microscopy 345
2.1.3. Fluorescence microscopy 346
3. Imaging of modified and functionally engaged nucleosomes 347
3.1. Imaging acetylated nucleosomes 347
3.2. Imaging transcriptionally active nucleosomes 347
3.3. Imaging remodeled nucleosomes 349
3.4. Imaging exchange of core and linker histones 350
4. Perspectives on the organization of the 30 nm fiber from
imaging approaches 352
5. Chromatin organization in the nucleus 355
5.1. Nuclear positioning of transcribed genes 357
5.2. Role of sub nuclear domains in establishing nuclear activity . . . 357
5.3. Dynamics of exchange of regulatory factors with
transcriptionally active genes 360
5.4. Imaging condensation/decondensation as a function of
gene activity 361
6. Summary 363
References 364
Chapter 14. Chromatin structure and dynamics: lessons from single molecule
approaches
Jordanka Zlatanova and Sanford H. Leuba 369
1. Introduction 369
2. Atomic force microscope imaging of chromatin fibers 370
2.1. AFM assessment of chromatin organization 371
2.2. AFM studies of biochemically manipulated or reconstituted
chromatin fibers 378
2.3. AFM assessment of structural effects of histone
post translational modifications 380
2.4. AFM visualization of salt induced chromatin fiber
compaction 381
3. Chromatin fiber assembly under applied force 382
4. Chromatin fiber disassembly under applied force 387
5. Summary 393
Acknowledgements 393
References 394
Chapter 15. Theory and computational modeling of the 30 nm
chromatin fiber
Jorg Langowski and Helmut Schiessel 397
1. Introduction 397
2. Physical properties of nucleosomes and DNA 399
xxi
3. Computational implementation 400
4. Energetics: coarse graining and interaction potentials 401
5. Mechanics of the chromatin fiber 402
5.1. The two angle model—basic notions 403
6. The chromatin chain at thermodynamic equilibrium 408
6.1. Metropolis Monte Carlo 408
6.2. Brownian dynamics simulation 409
7. Monte Carlo modeling of the chromatin fiber 410
7.1. Simulation of chromatin stretching 411
8. Dynamic simulations of the chromatin fiber 413
8.1. Brownian dynamics models of the chromatin fiber 413
9. The flexibility of the 30 nm fiber 414
9.1. Conclusion 415
References 416
Chapter 16. Nucleosome remodeling
Andrew A. Travers and Tom Owen Hughes 421
1. Introduction 421
2. Nucleosome mobility 421
3. Interactions of remodeling complexes 430
3.1. Common motifs and subunits in remodeling complexes 431
3.2. Interactions between remodeling complexes and nucleosomes . . . 433
4. Mechanism of remodeling 433
4.1. The mechanics of remodeling 433
4.2. DNA translocation and chromatin remodeling 436
4.3. The DNA topology of remodeling 440
4.4. Nucleosome priming 441
4.5. An active role for core histones in remodeling? 442
5. Biological functions of chromatin remodeling 444
5.1. General functions of remodeling complexes 445
5.2. Targeting of remodeling complexes 446
5.3. Nucleosome remodeling during transcription 447
5.4. Regulation of remodeling complexes 448
6. Endnote 449
Acknowledgements 449
References 449
Chapter 17. What happens to nucleosomes during transcription?
Vaughn Jackson 467
1. Introduction 467
2. In vivo studies of transcription on nucleosomes 467
2.1. Nuclease studies 467
2.2. Histones of active genes 469
2.3. In vivo nucleosomal dynamics 472
xxii
3. In vitro studies of transcription on nucleosomes 474
3.1. The eucaryotic polymerases 474
3.2. The procaryotic polymerases 475
3.3. The spooling model 476
3.4. The disruptive model 479
3.5. Transcription induced topological effects 480
3.6. Histone chaperones that release H2A, H2B 481
3.7. The chiral transition of H3, H4 484
3.8. Histone acetylation 485
3.9. Histone HI 486
4. Summary 487
References 488
Subject Index 493
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| owner_facet | DE-703 DE-355 DE-BY-UBR DE-12 DE-19 DE-BY-UBM |
| physical | XXV, 507 S. Ill., graph. Darst. |
| publishDate | 2004 |
| publishDateSearch | 2004 |
| publishDateSort | 2004 |
| publisher | Elsevier |
| record_format | marc |
| series | New comprehensive biochemistry |
| series2 | New comprehensive biochemistry |
| spelling | Chromatin structure and dynamics state-of-the-art eds. J. Zlatanova ... 1. ed. Amsterdam [u.a.] Elsevier 2004 XXV, 507 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier New comprehensive biochemistry 39 Chromatine Chromatin Chromatin metabolism Chromatin ultrastructure Chromatin (DE-588)4010152-6 gnd rswk-swf Struktur (DE-588)4058125-1 gnd rswk-swf Histone (DE-588)4159992-5 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Chromatin (DE-588)4010152-6 s Struktur (DE-588)4058125-1 s DE-604 Histone (DE-588)4159992-5 s b DE-604 Zlatanova, Jordanka Sonstige oth New comprehensive biochemistry 39 (DE-604)BV000003914 39 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010774291&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Chromatin structure and dynamics state-of-the-art New comprehensive biochemistry Chromatine Chromatin Chromatin metabolism Chromatin ultrastructure Chromatin (DE-588)4010152-6 gnd Struktur (DE-588)4058125-1 gnd Histone (DE-588)4159992-5 gnd |
| subject_GND | (DE-588)4010152-6 (DE-588)4058125-1 (DE-588)4159992-5 (DE-588)4143413-4 |
| title | Chromatin structure and dynamics state-of-the-art |
| title_auth | Chromatin structure and dynamics state-of-the-art |
| title_exact_search | Chromatin structure and dynamics state-of-the-art |
| title_full | Chromatin structure and dynamics state-of-the-art eds. J. Zlatanova ... |
| title_fullStr | Chromatin structure and dynamics state-of-the-art eds. J. Zlatanova ... |
| title_full_unstemmed | Chromatin structure and dynamics state-of-the-art eds. J. Zlatanova ... |
| title_short | Chromatin structure and dynamics |
| title_sort | chromatin structure and dynamics state of the art |
| title_sub | state-of-the-art |
| topic | Chromatine Chromatin Chromatin metabolism Chromatin ultrastructure Chromatin (DE-588)4010152-6 gnd Struktur (DE-588)4058125-1 gnd Histone (DE-588)4159992-5 gnd |
| topic_facet | Chromatine Chromatin Chromatin metabolism Chromatin ultrastructure Struktur Histone Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010774291&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000003914 |
| work_keys_str_mv | AT zlatanovajordanka chromatinstructureanddynamicsstateoftheart |