Mechanisms of Gene Expression : Structure, Function and Evolution of the Basal Transcriptional Machinery

by Weinzierl, Robert O. J.

• ISBN13: 9781860941269
• ISBN10: 1860941265
• Format: Hardcover
• Copyright: 1999-08-01
• Publisher: World Scientific Pub Co Inc

Table of Contents

Preface	v
RNA Polymerases	1	(25)
The Evolutionary History of RNA Polymerases	1	(2)
Structure and Function of Cellular RNA Polymerase Subunits	3	(12)
Other RNA Polymerases	15	(5)
Conclusions	20	(6)
Basal Factors Recognize Promoters and Assemble the Pre-Initiation Transcription Complexes	26	(50)
σ Factors Recruit RNA Polymerases to Different Promoters and Assist Transcript Initiation	27	(5)
Simple Beginnings: The Archaeal TATA-Binding Protein (TBP)-TFB-RNAP Initiation Complex	32	(4)
Eukaryotic RNAPII Promoters: TATA-Boxes, Initiator Elements and TBP-Associated Factors Responsible for Sequence-Specific Recognition	36	(13)
Recruitment of RNAPII/TFIIF	49	(1)
Promoter Melting, Transcript Initiation and the Role of TFIIE and TFIIH	50	(3)
Re-initiation and Recycling of Basal Factors	53	(1)
Basal Factors Reorganize Promoter Topology	54	(2)
The RNAPII Holoenzyme	56	(9)
Conclusions	65	(11)
Gene-Specific Transcription Factors	76	(63)
Regulatory Roles of Gene-Specific Transcription Factors in Eukaryotes	78	(2)
Mapping of Regulatory Motifs in Eukaryotic Promoters	80	(4)
DNA-Binding Domains	84	(19)
Activation Domains	103	(12)
Functional Modifications of Gene-Specific Transcription Factors	115	(7)
Gene-Specific Transcription Factors Shape Overall Promoter Topology	122	(3)
Conclusions	125	(14)
Coactivators: Interface between Gene-Specific and Basal Transcription Factors	139	(48)
Direct Contacts between Gene-Specific Transcription Factors and RNA Polymerase in Bacteria	139	(5)
Direct Contacts between Eukaryotic Activators and Eukaryotic RNA Polymerases?	144	(2)
The Coactivator Concept in Eukaryotic Transcription	146	(3)
TFIID as a Specific Coactivator Complex	149	(9)
Tissue-Specific TFIID Complexes	158	(6)
Specialized Coactivator/Activator Systems	164	(6)
The RNAPII Holoenzyme Mediator Complex	170	(3)
General Cofactors. The USA Fraction	173	(1)
Conclusions	174	(13)
Control of RNA Elongation and Termination	187	(48)
Transcription Elongation: Basic Mechanisms	189	(5)
The Coding Regions of Genes Contain Transcription Pause and Arrest Sites	194	(5)
Control of Elongation `Competence' of RNAPII	199	(13)
Transcription Termination in Bacteria	212	(10)
Specific Termination of Transcription in Eukaryotes	222	(3)
Conclusions	225	(10)
RNAPI and RNAPIII Transcriptional Machineries	235	(41)
Evolutionary History of the Compartmentalization of Eukaryotic Transcriptional Machinery	235	(2)
Structure and Function of the RNAPI Transcriptional Machinery	237	(10)
Structure and Function of the RNAPIII Transcriptional Machinery	247	(9)
The `Grey Area' between the RNAPII and RNAPIII Transcription Systems: snRNA Genes in Higher Eukaryotes	256	(7)
Control of RNAPI and RNAPIII Transcriptional Machineries	263	(3)
Conclusions	266	(10)
Chromatin	276	(48)
The Evolutionary Origin of Chromatin	277	(4)
Nucleosome Structure and Function --- The Basics	281	(12)
Initiation of Gene-Specific Transcription in Chromatin	293	(9)
Chromatin Remodelling of Promoters Packed into Repressive Chromatin Complexes	302	(3)
Heritable Maintenance of Gene Expression States through Regulated Heterochromatinization	305	(3)
Constitutive Heterochromatin: A Transcriptional Graveyard for Most Genes!	308	(5)
Conclusions	313	(11)
Nuclear Matrix, Chromosome Scaffolds and Transcriptional Factories	324	(19)
What is Nuclear Matrix?	325	(1)
Biochemical Composition of the Nuclear Matrix	326	(4)
The Nuclear Matrix Organizes Eukaryotic Chromatin into Higher Order Structures	330	(7)
Conclusions	337	(6)
Gene Expression Dynamics and Global Genome Transcription Patterns	343	(33)
The Molecular Quest for Global Genome Transcription Patterns	344	(2)
`Proteome' Projects	346	(2)
Molecular Characterization of Complex mRNA Populations	348	(13)
Detection of Genetic Regulatory Circuits and Identification of Target Genes	361	(4)
Defining Genome Transcription Patterns of Single Cells	365	(3)
The Ultimate Aim: Monitoring Gene Expression in Real Time	368	(3)
Conclusions	371	(5)
Appearing on the Horizon: Medical Applications Focusing on Transcriptional Control Mechanisms	376	(41)
The Need for Drugs Affecting Gene Expression Patterns	376	(2)
Strategies for Identifying Drugs Interfering with Gene-Specific Transcriptional Regulators	378	(10)
Reprogramming Transcription Patterns I: Drugs that Control Expression of Genes In Vivo	388	(7)
Reprogramming Transcription Patterns II: Drug-Mediated Activation of Alternate Members of Multigene Families	395	(4)
Nucleic Acid-Based Gene-Specific Therapeutic Agents	399	(7)
Drugs that Control Gene Transcription by Indirect Means	406	(11)
Index	417