Adhya / Garges RNA Polymerase and Associated Factors, Part D

1. Auflage 2003
ISBN: 978-0-08-052260-9
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 371, 674 Seiten, Web PDF

Reihe: Methods in Enzymology

RNA polymerase is molecule important to gene transcription. Along with associated factors, RNA polymerase is part of the process in which RNA is transcribed to produce a protein.* Models and methods for studying polymerase translocation* Assay for movements of RNA polymerase along DNA* Engineering of elongation complexes of bacterial and yeast RNA polymerases

Autoren/Hrsg.

Adhya, Sankar

Garges, Susan

Inhaltsverzeichnis

1;Cover;1
2;Title Page;4
3;Copyright Page;5
4;Table of Contents;6
5;Contributors to Volume 371;12
6;Volumes in Series;20
7;Section I: Transcription Elongation;42
7.1;Chapter 1. On Models and Methods for Studying Polymerase Translocation;44
7.2;Chapter 2. Evaluation of Fluorescence Spectroscopy Methods for Mapping Melted Regions of DNA Along the Transcription Pathway;54
7.3;Chapter 3. Single DNA Molecule Analysis of Transcription Complexes;75
7.4;Chapter 4. Assay for Movements of RNA Polymerase along DNA;91
7.5;Chapter 5. Kinetics of Multisubunit RNA Polymerases: Experimental Methods and Data Analysis;112
7.6;Chapter 6. Principles and Methods of Affinity Cleavage in Studying Transcription;123
7.7;Chapter 7. Iodine-125 Radioprobing of E. coli RNA Polymerase Transcription Elongation Complexes;147
7.8;Chapter 8. Formation of Long DNA Templates Containing Site-Specific Alkane–Disulfide DNA Interstrand Cross-Links for Use in Transcription Reactions;161
7.9;Chapter 9. Probing the Organization of Transcription Complexes Using Photoreactive 4-Thio- Substituted Analogs of Uracil and Thymidine;174
7.10;Chapter 10. Fluorescence Resonance Energy Transfer (FRET) in Analysis of Transcription- Complex Structure and Function;185
7.11;Chapter 11. Methods of Walking with the RNA Polymerase;201
7.12;Chapter 12. Stepwise Walking and Cross-Linking of RNA with Elongating T7 RNA Polymerase;211
7.13;Chapter 13. Characterization of Protein–Nucleic Acid Interactions that are Required for Transcription Processivity;220
7.14;Chapter 14. Strategies and Methods of Cross-Linking of RNA Polymerase Active Center;232
7.15;Chapter 15. Using a lac Repressor Roadblock to Analyze the E. Coli Transcription Elongation Complex;248
7.16;Chapter 16. Biochemical Assays of Gre Factors of Thermus Thermophilus;260
7.17;Chapter 17. Engineering of Elongation Complexes of Bacterial and Yeast RNA Polymerases;274
7.18;Chapter 18. Assay of Transient State Kinetics of RNA Polymerase II Elongation;293
7.19;Chapter 19. Analysis of RNA Polymerase II Elongation In vitro;305
7.20;Chapter 20. Preparation and Assay of RNA Polymerase II Elongation Factors Elongin and ELL;317
7.21;Chapter 21. Use Of RNA Yeast Polymerase II Mutants in Studying Transcription Elongation;325
7.22;Chapter 22. Acetylation of Human AP-Endonuclease 1, A Critical Enzyme in DNA Repair and Transcription Regulation;333
7.23;Chapter 23. Characterization of Transcription-Repair Coupling Factors in E. Coli and Humans;341
7.24;Chapter 24. Techniques to Analyze the HIV-1 Tat and TAR RNA-Dependent Recruitment and Activation of the Cyclin T1:CDK9 (P-TEFb) Transcription Elongation Factor;365
8;Section II: Transcription Termination;378
8.1;Chapter 25. Assay of Intrinsic Transcription Termination by E. Coli RNA Polymerase on Single-Stranded and Double-Stranded DNA Templates;380
8.2;Chapter 26. Bacteriophage HK022 Nun Protein: A Specific Transcription Termination Factor that Excludes Bacteriophage ;392
8.3;Chapter 27. Assay of Transcription Termination by Ribosomal Protein L4;397
8.4;Chapter 28. Analysis of the Intrinsic Transcription Termination Mechanism and Its Control;410
8.5;Chapter 29. Rho’s Role in Transcription Attenuation in the tna Operon of E. Coli;424
8.6;Chapter 30. Role of RNA Structure in Transcription Attenuation in Bacillus subtilis: The trpEDCFBA Operon as a Model System;433
8.7;Chapter 31. TRAP–RNA Interactions Involved in Regulating Transcription Attenuation of the Bacillus subtilis trp Operon;446
8.8;Chapter 32. Analyzing Transcription Antitermination in Lambdoid Phages Encoding Toxin Genes;459
8.9;Chapter 33. Genetic and Biochemical Strategies to Elucidate the Architecture and Targets of a Processive Transcription Antiterminator from Bacteriophage Lambda;479
8.10;Chapter 34. Assay of Transcription Antitermination by Proteins of the CspA Family;501
8.11;Chapter 35. Assay of Antitermination of Ribosomal RNA Transcription;513
9;Section III: Chromatin;530
9.1;Chapter 36. Purification of Elongating RNA Polymerase II and Other Factors from Yeast Chromatin;532
9.2;Chapter 37. Chromatin Assembly In Vitro with Purified Recombinant ACF and NAP-1;540
9.3;Chapter 38. Tying C’ Ends of H2A and H2B Using a Molecular Glue, Tissue-Type Transglutaminase;557
9.4;Chapter 39. Chromatin Decompaction Method by HMGN Proteins;562
9.5;Chapter 40. Assay of Activator Recruitment of Chromatin- Modifying Complexes;577
9.6;Chapter 41. Insights into Structure and Function of GCN5/ PCAF and yEsa 1 Histone Acetyltransferase Domains:;586
9.7;Chapter 42. Assay of the Fate of the Nucleosome During Transcription by RNA Polymerase II;605
9.8;Chapter 43. Probing Chromatin Immunoprecipitates with CpG-Island Microarrays to Identify Genomic Sites Occupied by DNA-Binding Proteins;618
9.9;Chapter 44. Isolation of RNA Polymerase Suppressors of a (p)ppGpp Deficiency;637
9.10;Chapter 45. Analysis of Transcriptional Repression by Mig1 in Saccharomyces cerevisiae Using a Reporter Assay;643
9.11;Chapter 46. Mutational Analysis of Drosphila RNA Polymerase II;656
10;Author Index;672
11;Subject Index;700