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
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