基因与信号

Preface
Foreword
Introduction
CHAPTER 1 Lessons from Bacteria
RNA POLYMERASE
REGULATED RECRUITMENT:THE/ac GENES
Protein-DNA Interactions
Detecting Physiological Signals
promoter Recognition and Transcription by RNA Polymerase
Switching the Genes On:Activation by CAP
Cooperative Binding of Proteins to DNA
Cooperative Binding and Gene Activation by CAP
Repression by Lac Repressor
Interim Summary and Extension
MORE REGULATED RECRUITMENT:THE BACTERIOPHAGE
The Switch
Establishing Lysogeny
Analogies with lac
promoters
Protein-DNA interactions
Repression
Activation
Detecting Physiological Signals
Making an Efficient Switch
Cooperative Binding of  Repressor to DNA
Autogenous Control by Repressor
PANEL:Antitermination:N and Q
Interim Summary and Extensions
Activation :A Closer Look
DNA binding:A Closer Look
Synergy
POLYMERASE ACTIVATION:glnA AND RELATED GENES
Promoter Recognition by  containing Ploymerase
DNA Binding by NtrC
Detecing the Physiological Signal
Activation by NtrC
Other Activatjors of Polymerase
Interim Summary
PANEL:Phage T4 Late Genes
PROMOTER ACTIVATION:merT AND RELATED GENES
Promoter Recognition
Detection the Physiological and Activation
Interim Summary
GENERAL SUMMARY
PANEL:more on Repression in Bacteria
FOOTNOTES
BIBLIOGRAPHY
CHAPTER 2 Yeast:A single-celled Eukaryote
RNA POLYMERASE
OTHER PARTS OF THE TRANSCRIPTIONAL MACHINERY
AN OVERVIEW OF ACTIVATION
A MODEL CASE: THE GAL GENES
Overview of Regulation of GAL Gene
Specific DNA Binding
Detecting Physiological Signals
HWO Gal4 WORKS
Separate DNA-binding and Activating Regions of Gal4
Activating Region Structure
Independent Mutations Can Increase Activator Stregth Additively When Combinde
Activation Regions Work with an Efficiency Proportional to Their Lengths
Activating Region-Target Interactions Tolerate Sequence Changes
New Activating Regions Are Easily Generated
Squelching
Recruitment Visualized
Activator Bypass Experiments
Activation by Heterologous Protein-Protein Interaction
Direct Tethering of the Transcriptional Machinery
PANEL:Activator Bypass Experiments
How does Gal4 Recruit Polymerase
nucleosomes and Their Modifiers
Targets of Gal4:Experiments Performed In Vitro
Action of Gal4:Experiments Performed In Vivo
What Is Required ofr Activation
What Appears at the Gene Upon Activation
Imposing a Need for Nucleosome Modifiers
Weakening the Gal4-binding Sites or the Gal4-activating region
Cell-cycle Stage-dependent Requirement for Nucleosome Modifiers
Activation:An Interim Summary
Repression by Mig1
SIGNAL INTERATION AND COMBINATIORAL CONTROL
Cooperative Binding with Alternative Partners
Sepuential Binding of Activators
SILENCING
Heterochromatic Chromosomal Regions
Compartmentalization
PANEL:Variegation Visualized
PANEL:Epigenetics
DNA LOOPING
SUMMARY
FOOTONTES
IBLIOGRAPHY
CHAPTER 3 Some Note on Higher Eukaryotes
MECHANISM OF ACTIVATION:RECRUITMENT
WHAT IS RECRUITES
Transcriptional Machinery and Promoters
Nucleosomal Templates
Targets
The Human Interferon-ß Gene
The Drosophila HSP70 Gene
REPRESSION
DETECTING AND TRANSMITTING PHYSIOLOGICAL SIGNALS
Transport Into and Out of the Nucleus
Phosphorylation of Inhibitor or Activatior in the Nucleus
PANEL:Tranport-dependent Proteolysis:The Case of SREBP
Allosteric Change of DNA-bound Activator
SIGNAL INTEGRATION,COMBINATIORIAL CONTROL,AND ALTERNATIVE ENHANCERS
The Human Interferon-ß Enhancer
The Drosophila eve Gene
ACTION AT A DISTANCE
DNA METHYLATION,INSULATORS,AND IMPRINTING
CHROMOSOMAL POSITION AND GENE EXPRESSION
COMPARTMENTALIZATION
OVERVIEW
FOOTNOTES
BIBLIOGRAPHY
CHAPTER 4 Enyme Specificity and Regulation
UBIQUITYLATION AND PROTEOLYSIS
SPLICING
IMPOSING SPECIFICITY ON KINASES
Cyclin-dependent kinases
Trascriptional Antitermination by TAT
Cytokine Receptors and Signaling through STATs
Growth Factor Receptors
INTERIM SUMMARY AND EXTENSION
Kinases
Phosphatases
Interpretin Signals
FURTHER GENERALIZATIONS
Dangers
Interpretin Experiments
Benefits
FOOTNOTES
BIBLIOGRAPHY
Afterword
Appendices
Appendix1:More on Cooperativity
Apperdix2:Topogenic Sepuences
Appendix3:All-or-none Effects and Levels of Gene Expression
Index