Chromatin structure and gene expression:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2000
|
| Ausgabe: | 2. ed. |
| Schriftenreihe: | Frontiers in molecular biology
35 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXVI, 328 S. Ill., graph. Darst. |
| ISBN: | 0199638896 019963890X |
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| 650 | 4 | |a Chromatin |x genetics | |
| 650 | 4 | |a Gene Expression Regulation | |
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Datensatz im Suchindex
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|---|---|
| adam_text | Contents
Preface v
List of contributors xv
Abbreviations xxi
1 Nucleosome and chromatin structure 1
TIMOTHY J. RICHMOND AND JONATHAN WIDOM
1. Introduction: the essence of chromatin 1
2. Core histone proteins 1
2.1 Sequences 1
2.2 Domain structure 3
2.3 Heterodimeric histone pairs 3
2.4 Histone DNA interactions 4
3. Nucleosome core 4
3.1 Histone and DNA organization 4
3.2 Histone fold extensions 5
4. Histone HI and the nucleosome 6
4.1 Sequence and domain structure 6
4.2 Binding site in the nucleosome 6
4.3 Functional roles 7
5. Chromatin fibre in vitro and in situ 7
5.1 Models for chromatin fibre structure 7
5.2 Interactions stabilizing the chromatin fibre 12
6. Nucleosome positioning 12
6.1 What is nucleosome positioning? 12
6.2 Mechanistic basis of nucleosome positioning 13
7. Nucleosome dynamics 14
7.1 In vitro assays 14
7.2 Mechanisms of nucleosome site exposure and mobility 15
7.3 Site exposure and mobility in nuclear processes 17
8. Summary and discussion 17
References 19
2 DNA replication, nucleotide excision repair, and
nucleosome assembly 24
PAUL D. KAUFMAN AND GENEVIEVE ALMOUZNI
1. Introduction 24
2. Overview of eukaryotic DNA replication 24
2.1 Primer synthesis 25
2.2 Polymerase switching and maturation of Okazaki fragments 27
3. Overview of nucleotide excision repair (NER) 28
3.1 Specialized proteins for recognition and excision of damaged DNA 29
3.2 Recruitment of general replication proteins to seal gaps caused by repair 29
3.3 Restoration of chromatin organization after DNA repair 29
4. Histones, nucleosome formation, and chromatin maturation 30
4.1 In vitro reconstitution of nucleosomal core particles 30
4.2 Coordination of histone deposition with DNA synthesis in vivo 30
4.3 Synthesis and modification of histones prior to assembly 32
5. In vitro nucleosome assembly systems unlinked to DNA synthesis 32
6. In vitro histone deposition systems linked to DNA synthesis 34
6.1 Replication and repair linked nucleosome assembly by cellular extracts 34
6.2 Chromatin assembly factor I (CAF I): biochemical functions 34
6.3 Primary structure and conservation of CAF I subunits 36
6.4 CAF I interacting proteins: histones H3 / H4, PCNA, and MODI 37
6.5 Stimulation of CAF I activity by ASF1 38
7. In vivo experiments with histone deposition proteins 39
7.1 Regulation and modification of CAF I during the cell cycle 39
7.2 Silencing and growth phenotypes of yeast cells lacking CAF I, Hir
proteins, and Asf 1 40
7.3 DNA repair defects of yeast cells lacking CAF 1 and Asf 1 41
8. Final comments 41
8.1 Important questions 41
8.2 Discussion 42
Acknowledgements 43
References 43
3 Chromatin structure and control of transcription in vivo 49
WOLFRAM HORZ AND SHARON ROTH
1. Introduction 49
2. Chromatin and transcription 49
2.1 Transcription by RNA polymerase II 49
2.2 Alterations in chromatin associated with transcription 50
2.3 Hallmark features of transcriptionally active chromatin 52
3. Mechanism of chromatin remodelling at the PHO5 and PHO8
promoters 53
3.1 Transcription factors involved in PHO5 regulation 53
3.2 The PHO5 chromatin transition 54
3.3 The Pho4 activation domain is required for chromatin remodelling
at the PHO5 promoter 55
3.4 SAGA and SWI/SNF are not needed for chromatin opening at the
PHO5 promoter 56
3.5 The related PHO8 promoter requires Gcn5 and Snf2 for remodelling 57
4. Repression by Ssn6 Tupl 58
4.1 Histones H3 and H4 are required for repression by Ssn6 Tupl 59
4.2 Acetylation of H3 and H4 antagonizes Ssn6 Tupl functions 60
4.3 Transcription factors also contribute to Ssn6 Tupl repression 61
5. Summary 61
5.1 Important questions 61
5.2 Discussion 64
References 65
4 The genetics of chromatin function 71
FRED WINSTON AND M. MITCHELL SMITH
1. Introduction 71
2. Histone gene organization in S. cerevisiae 72
2.1 The major core histone genes 72
2.2 Variant histone genes 72
3. Large transcription complexes that control chromatin structure 72
3.1 The Snf/Swinucleosome remodelling complex 73
3.2 The Spt Ada Gcn5 acetyltransferase (SAGA) complex 78
3.3 Genetic interactions between Snf / Swi and SAGA 81
3.4 Summary and conclusions 82
4. Genetic analysis of histone function 82
4.1 Mutations in the core histone tails 82
4.2 Mutations in the structured domains 85
4.3 Mutations in the dimer tetramer interfaces 87
4.4 Histone variant nucleosomes and transcription 89
5. Final comments 90
6. Discussion 90
Acknowledgements 91
References 91
5 The SWI/SNF family of remodelling complexes 97
BRADLEY R. CAIRNS AND ROBERT E. KINGSTON
1. Introduction 97
2. Structure/function of the SWI/SNF family 98
2.1 Isolation of the SWI / SNF family of remodellers 98
2.2 Subunits of SWI/SNF related complexes 99
2.3 ATP dependent remodelling activities of SWI / SNF family complexes 101
3. Targeting of SWI/SNF activity 106
4. Timing of SWI/SNF function 107
5. Maintaining active transcription 108
6. Regulation of SWI/SNF across the cell cycle 108
7. Connections of SWI/SNF complex to cancer 109
8. Summary and discussion 109
References 110
6 ATP dependent chromatin remodelling by the ISWI
complexes 114
CARL WU, PETER B. BECKER, AND TOSHIO TSUKIYAMA
1. Introduction 114
2. Biochemical assays for remodelling factors using nucleosome arrays 115
2.1 Promoter specific remodelling in concert with DNA binding proteins 116
2.2 Increased global accessibility to restriction enzymes 118
2.3 Imposition of regular spacing on nucleosome array 118
3. ISWI remodelling complexes purified from Drosophila, budding
yeast, and mammal 119
3.1 Structure of ISWI proteins 119
3.2 ISWI complexes from Drosophila 119
3.3 Yeast ISWI and ISW2 complexes 121
3.4 Human ISWI complexes 121
3.5 Related remodelling factors 122
4. Mechanism of nucleosome remodelling—catalysed mobility of
histone octamers 122
4.1 General considerations 122
4.2 Histone octamer sliding 123
4.3 ISWI is the engine of nucleosome mobility 124
4.4 Similarities and differences in remodelling by ISWI and SWF/SNF like
complexes 125
5. Nucleosome mobility can potentially affect nuclear functions 126
5.1 Transcription of chromatin templates in vitro 126
5.2 T antigen dependent DNA replication 127
5.3 Assembly and spacing of nucleosomes 128
6. In vivo functions of ISWI 128
6.1 Physiological roles of yeast ISWI and ISW2 128
6.2 Drosophila ISWI is required for transcription and chromosome structure 129
7. Summary and discussion 129
Acknowledgements 130
References 130
7 Histone acetyltransf erase/transcription co activator
complexes 135
SHELLEY L. BERGER, PATRICK A. GRANT, JERRY L. WORKMAN, AND
C. DAVID ALLIS
1. Introduction 135
2. Histone acetyltransf erase complexes 135
2.1 The elusive search for histone acetyltransferases 135
2.2 The diversity of histone acetyltransferases 136
2.3 Gcn5/PCAF containing HAT complexes 137
2.4 Other co activator HAT complexes 139
3. Functions of HAT complexes and histone acetylation 140
3.1 Recruitment of HAT complexes to target genes 140
3.2 Effects of histone acetylation 141
4. Other substrates of histone acetyltransferases 143
4.1 HATs as FATs (factor acetyltransferases) 143
4.2 FAT substrates. 143
4.3 Additional important questions regarding factor acetylation 145
5. Additional histone modifications: looking ahead 146
6. Discussion 147
Acknowledgements 148
References 148
8 Histone deacetylation: mechanisms of repression 156
ANDREW FREE, MICHAEL GRUNSTEIN, ADRIAN BIRD, AND MARIA VOGELAUER
1. Introduction and general remarks 156
2. Histone deacetylases and their complexes 156
2.1 Histone deacetylase enzymes in yeast and mammals 156
2.2 Histone deacetylases are members of multiprotein complexes 158
2.3 The SIR2 protein: a unique NAD dependent histone deacetylase 159
3. Heterochromatin and hypoacetylation 160
3.1 Yeast models of heterochromatin (telomeric, mating type, and
ribosomal DNA silencing) 160
3.2 Higher eukaryotic heterochromatin and hypoacetylation 163
3.3 Hypoacetylation of the inactive X chromosome in mammals 165
4. Deacetylation and repression of euchromatic genes 166
4.1 Recruitment of HDAC complexes to yeast promoters 166
4.2 Recruitment of HDAC complexes to mammalian promoters 167
4.3 Non promoter acetylation and deacetylation 168
5. DNA methylation and chromatin structure 170
5.1 Repression mediated by DNA methylation 170
5.2 Chromatin and methylation dependent repression 171
5.3 MeCP2, MBD2 and MBD1 are HDAC dependent silencers 172
5.4 Other links between DNA methylation and histone deacetylation 174
6. Final comments 174
References 175
9 Developmental regulation of chromatin function and
gene expression 182
ALAN P. WOLFFE AND MICHELLE CRAIG BARTON
1. Introduction 182
2. Chromatin structure and gene regulation during red cell development 182
2.1 Tissue specific expression and chromatin structure of the globin locus 184
2.2 Developmentally regulated chromatin structure and globin expression 186
2.3 DNA binding proteins that perturb chromatin structure 187
2.4 Linking biochemical analyses with physiological significance 188
2.5 Mechanisms for establishing active chromatin structure 189
3. Amphibian metamorphosis and thyroid hormone receptor 192
3.1 Thyroid hormone receptor 192
3.2 Gene control through modification of chromatin targeted by the
thyroid hormone receptor 193
3.3 Transcriptional control during metamorphosis 197
4. Final comments 198
4.1 Mechanisms of gene regulation in chromatin 198
4.2 Discussion 198
References 199
10 Chromatin contributions to epigenetic transcriptional
states in yeast 203
LISA FREEMAN COOK, ROHINTON KAMAKAKA, AND LORRAINE PILLUS
1. Introduction 203
2. Position effect control and heterochromatin 203
2.1 Overview of silencing in S. cerevisiae 204
2.2 Similarities and differences in S. pontbe 206
2.3 Silencing in other yeasts 206
3. Silencing sequences and proteins 207
3.1 Silencers and silenced sequences 207
3.2 Silencer bound proteins 209
3.3 Silencing complexes: the Sir proteins 210
3.4 S. pombe silencing genes 212
3.5 Other regulators of silencing 213
4. Building and regulating silenced chromatin 213
4.1 The structure of silenced chromatin 213
4.2 Silencing domains and boundary elements 216
4.3 Assembling silenced chromatin 217
4.4 Regulating silenced chromatin by protein modification 219
5. Final comments 220
5.1 Silencing mechanisms and biological regulation 220
5.2 Discussion 221
Acknowledgements 221
References 222
11 Epigenetic regulation in Drosophila: unravelling the
conspiracy of silence 228
JOEL C. EISSENBERG, SARAH C. R. ELGIN, AND RENATO PARO
1. Introduction: chromatin structure and gene silencing 228
2. Heterochromatic position effect variegation 229
2.1 Gene silencing associated with chromosomal position 229
2.2 A mass action assembly model 232
2.3 Modifiers of heterochromatic silencing 234
2.4 Organization of heterochromatin 236
3. Maintaining gene expression patterns by the mechanism of cellular
memory 238
3.1 The Polycomb group and antipodal trithorax group of chromosomal
proteins 239
3.2 PcG multimeric protein complexes and the chromo domain 241
3.3 PcG response elements and DNA binding specificity 242
4. Final comments: important questions and discussion 245
Acknowledgements 246
References 246
12 Epigenetics in mammals 252
CHRISTOPHER J. SCHOENHERR AND SHIRLEY M. TILGHMAN
1. Introduction 252
2. Genomic imprinting 252
2.1 The discovery of genomic imprinting 252
2.2 The epigenetic mark in genomic imprinting 254
2.3 The Ipl H19 imprinted gene cluster: regulating enhancers 256
2.4 The Igf2r gene cluster: regulating anti sense transcripts 259
2.5 The Prader Willi/ Angelman imprinted gene cluster: long range
regulation 261
3. X chromosome inactivation 263
3.1 Introduction 263
3.2 Counting 264
3.3 Choice 265
3.4 Initiation 265
3.5 Propagation and maintenance of X chromosome inactivation 268
3.6 Stability of the inactive X chromosome 269
3.7 Imprinted X chromosome inactivation 269
4. Final comments 270
4.1 Future directions in genomic imprinting 270
4.2 Future directions in X chromosome inactivation 270
4.3 Concluding remarks 271
References 271
13 Chromatin boundaries 278
VICTOR G. CORCES AND GARY FELSENFELD
1. Introduction 278
2. Boundary elements: specific examples 280
2.1 Drosophila insulator elements in the hsp70 heat shock locus 280
2.2 Drosophila insulator elements: the bithorax complex 283
2.3 Drosophila insulator elements: the gypsy retrovirus 283
2.4 Vertebrate insulator elements: globin locus boundary elements,
BEAD, RO, MARs, and others 285
2.5 Yeast boundary elements 289
3. Mechanisms 290
3.1 Relationship to mechanisms of enhancer action 290
3.2 Loop or domain models 291
4. Future questions 293
4.1 How does activation and deactivation over long distances work in
higher eukaryotes? 293
4.2 Are there any common patterns of action shared by the insulator
elements so far identified? Are there many more kinds of insulator
elements? 294
4.3 What cofactors are involved in establishing boundaries, and what
is their relationship to chromatin structure? 294
References 295
14 Linking large scale chromatin structure with nuclear
function 300
NICOLA L. MAHY, WENDY A. BICKMORE, TUDORITA TUMBAR, AND
ANDREW S. BELMONT
1. Introduction: why study large scale chromatin/chromosome
structure? 300
2. Comparing large scale chromatin structure within mitotic and
interphase chromosomes 300
2.1 Lessons from model, non mitotic chromosomes 301
2.2 Models of mitotic and interphase chromosome structure 302
3. Organization of chromosomes within the interphase nucleus 304
3.1 Chromosome territories and intermingling between chromosomes 304
3.2 Spatial distribution of chromosomes relative to each other 304
3.3 Spatial distribution of chromosomes and chromosome domains
relative to nuclear landmarks 305
4. Evidence for the role of large scale chromatin structure in regulation 306
4.1 Chromatin compaction 307
4.2 Does replication timing dictate the formation of distinct chromatin
domains? 308
4.3 Localization of sites of transcription 309
4.4 Are active genes displayed on the surface of chromosome territories? 309
4.5 Positioning of specific genes relative to nuclear bodies 310
4.6 Sites of transcriptional repression within the nucleus 310
5. Dynamics of large scale organization 311
5.1 Cell cycle changes 311
5.2 Quiescence and senescence 313
5.3 Differentiation 314
6. Final comments 314
Acknowledgements 315
References 315
Index 323
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| id | DE-604.BV013498046 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:46:52Z |
| institution | BVB |
| isbn | 0199638896 019963890X |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-009213601 |
| oclc_num | 44885388 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-634 DE-11 |
| owner_facet | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-634 DE-11 |
| physical | XXVI, 328 S. Ill., graph. Darst. |
| publishDate | 2000 |
| publishDateSearch | 2000 |
| publishDateSort | 2000 |
| publisher | Oxford Univ. Press |
| record_format | marc |
| series | Frontiers in molecular biology |
| series2 | Frontiers in molecular biology |
| spelling | Chromatin structure and gene expression ed. by Sarah C. R. Elgin ... 2. ed. Oxford [u.a.] Oxford Univ. Press 2000 XXVI, 328 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Frontiers in molecular biology 35 Chromatine Chromatine gtt Genexpressie gtt Chromatin Chromatin genetics Gene Expression Regulation Struktur (DE-588)4058125-1 gnd rswk-swf Chromatin (DE-588)4010152-6 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Chromatin (DE-588)4010152-6 s Struktur (DE-588)4058125-1 s Genexpression (DE-588)4020136-3 s DE-604 DNS (DE-588)4070512-2 s 1\p DE-604 Elgin, Sarah C. R. Sonstige oth Frontiers in molecular biology 35 (DE-604)BV010329078 35 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009213601&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Chromatin structure and gene expression Frontiers in molecular biology Chromatine Chromatine gtt Genexpressie gtt Chromatin Chromatin genetics Gene Expression Regulation Struktur (DE-588)4058125-1 gnd Chromatin (DE-588)4010152-6 gnd Genexpression (DE-588)4020136-3 gnd DNS (DE-588)4070512-2 gnd |
| subject_GND | (DE-588)4058125-1 (DE-588)4010152-6 (DE-588)4020136-3 (DE-588)4070512-2 |
| title | Chromatin structure and gene expression |
| title_auth | Chromatin structure and gene expression |
| title_exact_search | Chromatin structure and gene expression |
| title_full | Chromatin structure and gene expression ed. by Sarah C. R. Elgin ... |
| title_fullStr | Chromatin structure and gene expression ed. by Sarah C. R. Elgin ... |
| title_full_unstemmed | Chromatin structure and gene expression ed. by Sarah C. R. Elgin ... |
| title_short | Chromatin structure and gene expression |
| title_sort | chromatin structure and gene expression |
| topic | Chromatine Chromatine gtt Genexpressie gtt Chromatin Chromatin genetics Gene Expression Regulation Struktur (DE-588)4058125-1 gnd Chromatin (DE-588)4010152-6 gnd Genexpression (DE-588)4020136-3 gnd DNS (DE-588)4070512-2 gnd |
| topic_facet | Chromatine Genexpressie Chromatin Chromatin genetics Gene Expression Regulation Struktur Genexpression DNS |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009213601&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV010329078 |
| work_keys_str_mv | AT elginsarahcr chromatinstructureandgeneexpression |