Chromatin Structure and Gene Expression

by Elgin, Sarah C. R.; Workman, Jerry L.

• ISBN13: 9780199638901
• ISBN10: 019963890X
• Edition: 2nd
• Format: Paperback
• Copyright: 2001-02-15
• Publisher: Oxford University Press

Summary

Since publication of the first edition in 1995, there have been significant advances and understanding of chromatin structure and its relation to gene expression. These include a high-resolution structure of the nucleosome core, discovery of the enzymes and complexes that mediate histoneacetylation and deacetylation, discovery of novel ATP-dependent chromatin remodeling complexes, new insights into nuclear organization and epigenetic silencing mechanisms. In light of these advances, Chromatin Structure and Gene Expression (2ed.) includes updated chapters and additional materialthat introduce new concepts in the process of gene regulation in chromatin.

Table of Contents

Preface	v
List of contributors	xv
Abbreviations	xxi
Nucleosome and chromatin structure	1	(23)
Timothy J. Richmond
Jonathan Widom
Introduction: the essence of chromatin	1	(1)
Core histone proteins	1	(3)
Sequences	1	(2)
Domain Structure	3	(1)
Heterodimeric histone pairs	3	(1)
Histone-DNA interactions	4	(1)
Nucleosome core	4	(2)
Histone and DNA organization	4	(1)
Histone-fold extensions	5	(1)
Histone H1 and the nucleosome	6	(1)
Sequence and domain structure	6	(1)
Binding site in the nucleosome	6	(1)
Functional roles	7	(1)
Chromatin fibre in vitro and in situ	7	(5)
Models for chromatin fibre structure	7	(5)
Interactions stabilizing the chromatin fibre	12	(1)
Nucleosome positioning	12	(2)
What is nucleosome positioning?	12	(1)
Mechanistic basis of nucleosome positioning	13	(1)
Nucleosome dynamics	14	(3)
In vitro assays	14	(1)
Mechanisms of nucleosome site exposure and mobility	15	(2)
Site exposure and mobility in nuclear processes	17	(1)
Summary and discussion	17	(7)
References	19	(5)
DNA replication, nucleotide excision repair, and nucleosome assembly	24	(25)
Paul D. Kaufman
Genevieve Almouzni
Introduction	24	(1)
Overview of eukaryotic DNA replication	24	(4)
Primer synthesis	25	(2)
Polymerase switching and maturation of Okazaki fragments	27	(1)
Overview of nucleotide excision repair (NER)	28	(2)
Specialized proteins for recognition and excision of damaged DNA	29	(1)
Recruitment of general replication proteins to seal gaps caused by repair	29	(1)
Restoration of chromatin organization after DNA repair	29	(1)
Histones, nucleosome formation, and chromatin maturation	30	(2)
In vitro reconstitution of nucleosomal core particles	30	(1)
Coordination of histone deposition with DNA synthesis in vivo	30	(2)
Synthesis and modification of histones prior to assembly	32	(1)
In vitro nucleosome assembly systems unlinked to DNA synthesis	32	(2)
In vitro histone deposition systems linked to DNA synthesis	34	(5)
Replication and repair-linked nucleosome assembly by celluar extracts	34	(1)
Chromatin assembly factor-I (CAF-I): biochemical functions	34	(2)
Primary structure and conservation of CAF-I subunits	36	(1)
CAF-I interacting proteins: histones H3/H4, PCNA, and MODI	37	(1)
Stimulation of CAF-I activity by ASF1	38	(1)
In vivo experiments with histone deposition proteins	39	(2)
Regulation and modification of CAF-I during the cell cycle	39	(1)
Silencing and growth phenotypes of yeast cells lacking CAF-I, Hir proteins, and Asf1	40	(1)
DNA repair defects of yeast cells lacking CAF-1 and Asf1	41	(1)
Final comments	41	(8)
Important questions	41	(1)
Discussion	42	(1)
Acknowledgements	43	(1)
References	43	(6)
Chromatin structure and control of transcription in vivo	49	(22)
Wolfram Horz
Sharon Roth
Introduction	49	(1)
Chromatin and transcription	49	(4)
Transcription by RNA polymerase II	49	(1)
Alterations in chromatin associated with transcription	50	(2)
Hallmark features of transcriptionally active chromatin	52	(1)
Mechanism of chromatin remodelling at the PHO5 and PHO8 promoters	53	(5)
Transcription factors involved in PHO5 regulation	53	(1)
The PHO5 chromatin transition	54	(1)
The Pho4 activation domain is required for chromatin remodelling at the PHO5 promoter	55	(1)
SAGA and SWI/SNF are not needed for chromatin opening at the PHO5 promoter	56	(1)
The related PHO8 promoter requires Gen5 and Snf2 for remodelling	57	(1)
Repression by Ssn6-Tup1	58	(3)
Histones H3 and H4 are required for repression by Ssn6-Tup1	59	(1)
Acetylation of H3 and H4 antagonizes Ssn6-Tup1 functions	60	(1)
Transcription factors also contribute to Ssn6-Tup1 repression	61	(1)
Summary	61	(10)
Important questions	61	(3)
Discussion	64	(1)
References	65	(6)
The genetics of chromatin function	71	(26)
Fred Winston
M. Mitchell Smith
Introduction	71	(1)
Histone gene organization in S. cerevisiae	72	(1)
The major core histone genes	72	(1)
Variant histone genes	72	(1)
Large transcription complexes that control chromatin structure	72	(10)
The Snf/Swi nucleosome remodelling complex	73	(5)
The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex	78	(3)
Genetic interactions between Snf/Swi and SAGA	81	(1)
Summary and conclusions	82	(1)
Genetic analysis of histone function	82	(8)
Mutations in the core histone tails	82	(3)
Mutations in the structured domains	85	(2)
Mutations in the dimer-tetramer interfaces	87	(2)
Histone-variant nucleosomes and transcription	89	(1)
Final comments	90	(1)
Discussion	90	(7)
Acknowledgements	91	(1)
References	91	(6)
The SWI/SNF family of remodelling complexes	97	(17)
Bradley R. Cairns
Robert E. Kingston
Introduction	97	(1)
Structure/function of the SWI/SNF family	98	(8)
Isolation of the SWI/SNF family of remodellers	98	(1)
Subunits of SWI/SNF-related complexes	99	(2)
ATP-dependent remodelling activities of SWI/SNF family complexes	101	(5)
Targeting of SWI/SNF activity	106	(1)
Timing of SWI/SNF function	107	(1)
Maintaining active transcription	108	(1)
Regulation of SWI/SNF across the cell cycle	108	(1)
Connections of SWI/SNF complex to cancer	109	(1)
Summary and discussion	109	(5)
References	110	(4)
ATP-dependent chromatin remodelling by the ISWI complexes	114	(21)
Carl WU
Peter B. Becker
Toshio Tsukiyama
Introduction	114	(1)
Biochemical assays for remodelling factors using nucleosome arrays	115	(4)
Promoter-specific remodelling in concert with DNA-binding proteins	116	(2)
Increased global accessibility to restriction enzymes	118	(1)
Imposition of regular spacing on nucleosome array	118	(1)
ISWI remodelling complexes purified from Drosophila, budding yeast, and mammal	119	(3)
Structure of ISWI proteins	119	(1)
ISWI complexes from Drosophila	119	(2)
Yeast ISWI and ISW2 complexes	121	(1)
Human ISWI complexes	121	(1)
Related remodelling factors	122	(1)
Mechanism of nucleosome remodelling---catalysed mobility of histone octamers	122	(4)
General considerations	122	(1)
Histone octamer sliding	123	(1)
ISWI is the engine of nucleosome mobility	124	(1)
Similarities and differences in remodelling by ISWI and SWF/SNF-like complexes	125	(1)
Nucleosome mobility can potentially affect nuclear functions	126	(2)
Transcription of chromatin templates in vitro	126	(1)
T-antigen-dependent DNA replication	127	(1)
Assembly and spacing of nucleosomes	128	(1)
In vivo functions of ISWI	128	(1)
Physiological roles of yeast ISW1 and ISW2	128	(1)
Drosophila ISWI is required for transcription and chromosome structure	129	(1)
Summary and discussion	129	(6)
Acknowledgements	130	(1)
References	130	(5)
Histone acetyltransferase/transcription co-activator complexes	135	(21)
Shelley L. Berger
Patrick A. Grant
Jerry L. Workman
C. David Allis
Introduction	135	(1)
Histone acetyltransferase complexes	135	(5)
The elusive search for histone acetyltransferases	135	(1)
The diversity of histon acetyltransferases	136	(1)
Gcn5/PCAF-containing HAT complexes	137	(2)
Other `co-activator' HAT complexes	139	(1)
Functions of HAT complexes and histone acetylation	140	(3)
Recruitment of HAT complexes to target genes	140	(1)
Effects of histone acetylation	141	(2)
Other substrates of histone acetyltransferases	143	(3)
HATs as FATs (factor acetyltransferases)	143	(1)
FAT substrates.	143	(2)
Additional important questions regarding factor acetylation	145	(1)
Additional histone modifications: looking ahead	146	(1)
Discussion	147	(9)
Acknowledgements	148	(1)
References	148	(8)
Histone deacetylation: mechanisms of repression	156	(26)
Andrew Free
Michael Grunstein
Adrian Bird
Maria Vogelauer
Introduction and general remarks	156	(1)
Histone deacetylases and their complexes	156	(4)
Histone deacetylase enzymes in yeast and mammals	156	(2)
Histone deacetylases are members of multiprotein complexes	158	(1)
The SIR2 protein: a unique NAD-dependent histone deacetylase	159	(1)
Heterochromatin and hypoacetylation	160	(6)
Yeast models of heterochromatin (telomeric, mating-type, and ribosomal DNA silencing)	160	(3)
Higher eukaryotic heterochromatin and hypoacetylation	163	(2)
Hypoacetylation of the inactive X chromosome in mammals	165	(1)
Deacetylation and repression of euchromatic genes	166	(4)
Recruitment of HDAC complexes to yeast promoters	166	(1)
Recruitment of HDAC complexes to mammalian promoters	167	(1)
Non-promoter acetylation and deacetylation	168	(2)
DNA methylation and chromatin structure	170	(4)
Repression mediated by DNA methylation	170	(1)
Chromatin and methylation-dependent repression	171	(1)
MeCP2, MBD2 and MBD1 are HDAC-dependent silencers	172	(2)
Other links between DNA methylation and histone deacetylation	174	(1)
Final comments	174	(8)
References	175	(7)
Developmental regulation of chromatin function and gene expression	182	(21)
Alan P. Wolffe
Michelle Craig Barton
Introduction	182	(1)
Chromatin structure and gene regulation during red cell development	182	(10)
Tissue-specific expression and chromatin structure of the globin locus	184	(2)
Developmentally regulated chromatin structure and globin expression	186	(1)
DNA-binding proteins that perturb chromatin structure	187	(1)
Linking biochemical analyses with physiological significance	188	(1)
Mechanisms for establishing active chromatin structure	189	(3)
Amphibian metamorphosis and thyroid hormone receptor	192	(6)
Thyroid hormone receptor	192	(1)
Gene control through modification of chromatin targeted by the thyroid hormone receptor	193	(4)
Transcriptional control during metamorphosis	197	(1)
Final comments	198	(5)
Mechanisms of gene regulation in chromatin	198	(1)
Discussion	198	(1)
References	199	(4)
Chromatin contributions to epigenetic transcriptional states in yeast	203	(25)
Lisa Freeman-Cook
Rohinton Kamakaka
Lorraine Pillus
Introduction	203	(1)
Position effect control and heterochromatin	203	(4)
Overview of silencing in S. cerevisiae	204	(2)
Similarities and differences in S. pombe	206	(1)
Silencing in other yeasts	206	(1)
Silencing sequences and proteins	207	(6)
Silencers and silenced sequences	207	(2)
Silencer-bound proteins	209	(1)
Silencing complexes: the Sir proteins	210	(2)
S. pombe silencing genes	212	(1)
Other regulators of silencing	213	(1)
Building and regulating silenced chromatin	213	(7)
The structure of silenced chromatin	213	(3)
Silencing domains and boundary elements	216	(1)
Assembling silenced chromatin	217	(2)
Regulating silenced chromatin by protein modification	219	(1)
Final comments	220	(8)
Silencing mechanisms and biological regulation	220	(1)
Discussion	221	(1)
Acknowledgements	221	(1)
References	222	(6)
Epigenetic regulation in Drosophila: unravelling the conspiracy of silence	228	(24)
Joel C. Eissenberg
Sarah C. R. Elgin
Renato Paro
Introduction: chromatin structure and gene silencing	228	(1)
Heterochromatic position effect variegation	229	(9)
Gene silencing associated with chromosomal position	229	(3)
A mass-action assembly model	232	(2)
Modifiers of heterochromatic silencing	234	(2)
Organization of heterochromatin	236	(2)
Maintaining gene expression patterns by the mechanism of cellular memory	238	(7)
The Polycomb group and antipodal trithorax group of chromosomal proteins	239	(2)
PcG multimeric protein complexes and the chromo domain	241	(1)
PcG response elements and DNA-binding specificity	242	(3)
Final comments: important questions and discussion	245	(7)
Acknowledgements	246	(1)
References	246	(6)
Epigenetics in mammals	252	(26)
Christopher J. Schoenherr
Shirley M. Tilghman
Introduction	252	(1)
Genomic imprinting	252	(11)
The discovery of genomic imprinting	252	(2)
The epigenetic mark in genomic imprinting	254	(2)
The Ipl-H19 imprinted gene cluster: regulating enhancers	256	(3)
The Igf2r gene cluster: regulating anti-sense transcripts	259	(2)
The Prader-Willi/Angelman imprinted gene cluster: long-range regulation	261	(2)
X-chromosome inactivation	263	(7)
Introduction	263	(1)
Counting	264	(1)
Choice	265	(1)
Initiation	265	(3)
Propagation and maintenance of X-chromosome inactivation	268	(1)
Stability of the inactive X chromosome	269	(1)
Imprinted X-chromosome inactivation	269	(1)
Final comments	270	(1)
Future directions in genomic imprinting	270	(1)
Future directions in X-chromosome inactivation	270	(1)
Concluding remarks	271	(1)
References	271	(7)
Chromatin boundaries	278	(22)
Victor G. Corces
Gary Felsenfeld
Introduction	278	(2)
Boundary elements: specific examples	280	(10)
Drosophila insulator elements in the hsp70 heat-shock locus	280	(3)
Drosophila insulator elements: the bithorax complex	283	(1)
Drosophila insulator elements: the gypsy retrovirus	283	(2)
Vertebrate insulator elements: globin locus boundary elements, BEAD, RO, MARs, and others	285	(4)
Yeast boundary elements	289	(1)
Mechanisms	290	(3)
Relationship to mechanisms of enhancer action	290	(1)
Loop or domain models	291	(2)
Future questions	293	(7)
How does activation and deactivation over long distances work in higher eukaryotes?	293	(1)
Are there any common patterns of action shared by the insulator elements so far identified? Are there many more kinds of insulator elements?	294	(1)
What cofactors are involved in establishing boundaries, and what is their relationship to chromatin structure?	294	(1)
References	295	(5)
Linking large-scale chromatin structure with nuclear function	300	(23)
Nicola L. Mahy
Wendy A. Bickmore
Tudorita Tumbar
Andrew S. Belmont
Introduction: why study large-scale chromatin/chromosome structure?	300	(1)
Comparing large-scale chromatin structure within mitotic and interphase chromosomes	300	(4)
Lessons from model, non-mitotic chromosomes	301	(1)
Models of mitotic and interphase chromosome structure	302	(2)
Organization of chromosomes within the interphase nucleus	304	(2)
Chromosome territories and intermingling between chromosomes	304	(1)
Spatial distribution of chromosomes relative to each other	304	(1)
Spatial distribution of chromosomes and chromosome domains relative to nuclear landmarks	305	(1)
Evidence for the role of large-scale chromatin structure in regulation	306	(5)
Chromatin compaction	307	(1)
Does replication timing dictate the formation of distinct chromatin domains?	308	(1)
Localization of sites of transcription	309	(1)
Are active genes displayed on the surface of chromosome territories?	309	(1)
Positioning of specific genes relative to nuclear bodies	310	(1)
Sites of transcriptional repression within the nucleus	310	(1)
Dynamics of large-scale organization	311	(3)
Cell-cycle changes	311	(2)
Quiescence and senescence	313	(1)
Differentiation	314	(1)
Final comments	314	(9)
Acknowledgements	315	(1)
References	315	(8)
Index	323