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Transcriptional regulation in eukaryotes : concepts, strategies, and techniques / Michael F. Carey, Craig L. Peterson, Stephen T. Smale. — 2nd ed. — Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, c2009. – (58.174251/C275/2nd ed.) |
Contents
Contents
PREFACE， x
OVERVIEW， x
ABBREVIATIONS AND ACRONYMS， xv
1 A PRIMER ON TRANSCRIPTIONAL REGULATION IN MAMMALIAN CELLS
INTRODUCTION AND OVERVIEW， 1
CHROMATIN AND THE GENERAL TRANSCRIPTION MACHINERY， 5
ACTIVATION AND REPRESSION， 28
CONCLUDING PERSPECTIVE， 41
2 INITIAL STRATEGIC ISSUES
INTRODUCTION AND OVERVIEW， 47
EXPERIMENTAL STRATEGIES， 48
TECHNIQUES， 63
3 TRANSCRIPTION INITIATION SITE MAPPING
INTRODUCTION AND OVERVIEW， 71
EXPERIMENTAL STRATEGIES， 74
TECHNIQUES， 90
4 FUNCTIONAL ASSAYS FOR PROMOTER ANALYSIS
INTRODUCTION AND OVERVIEW， 107
EXPERIMENTAL STRATEGIES， 110
TECHNIQUES， 137
5 IDENTIFICATION AND ANALYSIS OF DISTANT CONTROL REGIONS
INTRODUCTION AND OVERVIEW， 161
EXPERIMENTAL STRATEGIES， 168
6 IDENTIFYING C/S-ACTING DNA ELEMENTS WITHIN A CONTROL REGION
INTRODUCTION AND OVERVIEW， 185
EXPERIMENTAL STRATEGIES， 187
7 IDENTIFICATION OF DNA-BINDING PROTEINS AND THEIR GENES
INTRODUCTION AND OVERVIEW， 205
EXPERIMENTAL STRATEGIES FOR THE IDENTIFICATION OF DNA-BINDING PROTEINS， 207
EXPERIMENTAL STRATEGIES FOR CLONING OR IDENTIFYING GENES ENCODING DNA-BINDING PROTEINS， 223
8 CONFIRMING THE FUNCTIONAL IMPORTANCE OF PROTEIN-DNA INTERACTION
INTRODUCTION AND OVERVIEW， 235
EXPERIMENTAL STRATEGIES， 237
9 IN VIVO ANALYSIS OF AN ENDOGENOUS CONTROL REGION
INTRODUCTION AND OVERVIEW， 261
EXPERIMENTAL STRATEGIES， 263
TECHNIQUES， 287
10 IDENTIFYING AND CHARACTERIZING DOMAINS OF TRANSCRIPTION REGULATORY FACTORS
INTRODUCTION AND OVERVIEW， 323
EXPERIMENTAL STRATEGIES: DEFINING DOMAINS， 324
CONCEPTS AND STRATEGIES: PROTEIN-PROTEIN INTERACTIONS， 342
TECHNIQUES， 356
11 DNA BINDING BY REGULATORY TRANSCRIPTION FACTORS
INTRODUCTION AND OVERVIEW， 367
EXPERIMENTAL STRATEGIES， 369
TECHNIQUES， 405
12 TRANSCRIPTION AND PREINITIATION COMPLEX ASSEMBLY IN VITRO
INTRODUCTION AND OVERVIEW， 439
EXPERIMENTAL STRATEGIES， 442
TECHNIQUES， 480
13 STUDYING CHROMATIN DYNAMICS IN VITRO: CHROMATIN ASSEMBLY， REMODELING， AND TRANSCRIPTION
INTRODUCTION AND OVERVIEW， 539
EXPERIMENTAL STRATEGIES， 541
TECHNIQUES， 573
APPENDIX: CAUTIONS， 605
INDEX， 613
