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Main description:
Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring in vivo protein-DNA interactions at any genomic loci. Transcriptional Regulation: Methods and Protocols takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world. Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls.
Comprehensive and accessible, Transcriptional Regulation: Methods and Protocols equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time.
Contents:
Part I: Promoter Elements, Transcription Factors, and Pre-Initiation Complex (PIC) Assembly
1. Genome Wide In Vivo Crosslinking of Sequence Specific Transcription Factors
Xiao-Yong Li and Mark D. Biggin
2. Characterization of Complex Regulatory Networks and Identification of Promoter Regulatory Elements in Yeast: "In Silico" and "Wet-Lab" Approaches
Nuno P. Mira, Miguel C. Teixeira, and Isabel Sa-Correia
3. Electrophoretic Mobility Shift Assay Analysis of NFkB Transcriptional Regulation by Nuclear IkBa
Ashish Juvekar, Sitharam Ramaswami, Subrata Manna, Tzu-Pei Chang, Adeel Zubair, and Ivana Vancurova
4. Probing Endogenous RNA Polymerase II Pre-Initiation Complexes by Electrophoretic Mobility Shift Assay
Emmanuelle Wilhelm, Christopher Takacs, and Brendan Bell
5. Elucidating Protein: DNA Complex by Oligonucleotide DNA Affinity Purification
Teddy T.C. Yang and Chi-Wing Chow
6. Chromatin Immunoprecipitation (ChIP) Assay as Tool for Analyzing Transcription Factor Activity
Padmaja Gade and Dhan V. Kalvakolanu
7. Two-Step Crosslinking for Analysis of Protein-Chromatin Interactions
Bing Tian, Jun Yang, and Allan R. Brasier
8. Chromatin Immunoprecipitation Analysis of NFkB Transcriptional Regulation by Nuclear IkBa in Human Macrophages
Sitharam Ramaswami, Subrata Manna, Ashish Juvekar, Steven Kennedy, Ales Vancura, and Ivana Vancurova
9. In Vivo ChIP for the Analysis of Microdissected Tissue Samples
Chris Murgatroyd, Anke Hoffmann, and Dietmar Spengler
10. Quantification of Protein-DNA Interactions by In Vivo Chromatin Immunoprecipitation in Yeast
Amparo Pascual-Ahuir and Markus Proft
11. Mapping Protein-DNA Interactions Using ChIP-Sequencing
Charles E. Massie and Ian G. Mills
12. ChIP and ReChIP Assays: Investigating Interactions Between Regulatory Proteins, Histone Modifications, and the DNA Sequences to which They Bind
Agnieszka D. Truax and Susanna F. Greer
13. Transcriptional Regulation of Genes Via Hypoxia-Inducible Factor
Olga Roche and Michael Ohh
14. Exchange Protein Directly Activated By Cyclic AMP 1 (Epac1)-Regulated Recruitment of CCAAT/Enhancer Binding Proteins (C/EBPs) to the Suppressor of Cytokine Signalling-3 (SOCS-3) Promoter
William A. Sands, Hayley D. Woolson, Stephen J. Yarwood, and Timothy M. Palmer
Part II: Chromatin Structure
15. Computational Analysis of Promoter Elements and Chromatin Features in Yeast
John J. Wyrick
16. Chromatin Affinity Purification (ChAP)
Ryoko Harada and Alain Nepveu
17. Determination of Histone Acetylation Status by Chromatin Immunoprecipitation
Luciano Galdieri, John Moon, and Ales Vancura
18. Immunostaining of Drosophila Polytene Chromosomes to Investigate Recruitment of Chromatin Binding Proteins
Magdalena Murawska and Alexander Brehm
19. Detection of Transcriptional Activators, Co-Activators, and Chromatin Remodeling by Chromatin Immunoprecipitation Coupled with Real-Time PCR
Tamara Y. Erkina and Alexandre M. Erkine
20. Chromatin Endogenous Cleavage and Psoralen Crosslinking Assays to Analyze rRNA Gene Chromatin In Vivo
Joachim Griesenbeck, Manuel Wittner, Romain Charton, and Antonio Conconi
21. UV-Induced DNA Damage and DNA Repair in Ribosomal Genes Chromatin
Julie Pelloux, Maxime Tremblay, Raymund J. Wellinger, and Antonio Conconi
22. Analysis of SUC2 Promoter Structure by Nucleosome Scanning
Jennifer Chang and Ales Vancura
23. Chromatin Immunoprecipitation of Mouse Embryos
Anne K. Voss, Mathew P. Dixon, Tamara McLennan, Andrew J. Kueh, and Tim Thomas
24. Chromatin Immunoprecipitation (ChIP) in Mouse Hippocampal Cells and Tissues
Badi Sri Sailaja, Takumi Takizawa, and Eran Meshorer
Part III: Chromatin Modifying Complexes
25. Approaches for Studying Nucleosome Movement by ATP-Dependent Chromatin Remodeling Complexes
Swetansu K. Hota and Blaine Bartholomew
26. Mapping Protein-DNA and Protein-Protein Interactions of ATP-Dependent Chromatin Remodelers
Swetansu K. Hota, Mekonnen Lemma Dechassa, Punit Prasad, and Blaine Bartholomew
27. Evaluation of Histone Modifying Enzymes in Stem Cell Populations
Leanne Stalker and Christopher Wynder
28. Purification of Multiprotein Histone Acetyltransferase Complexes
Yuan-Liang Wang, Francesco Faiola, and Ernest Martinez
29. Reconstitution of Active and Stoichiometric Multisubunit Lysine Acetyltransferase Complexes in Insect Cells
Kezhi Yan, Chao-Jung Wu, Nadine Pelletier, and Xiang-Jiao Yang
30. Affinity Purification of MLL3/MLL4 Histone H3K4 Methyltransferase Complex
Young-Wook Cho, SunHwa Hong, and Kai Ge
31. Methods for Analyzing Histone Citrullination in Chromatin Structure and Gene Regulation
Pingxin Li, Jing Hu, and Yanming Wang
Part IV: RNA Synthesis and Regulation
32. Analysis of mRNA Abundance and Stability by Ribonuclease Protection Assay
Cristina Romero-Lopez, Alicia Barroso-delJesus, Pablo Menendez, and Alfredo Berzal-Herranz
33. Array-Based Nuclear Run-On (ANRO) Analysis
Jinshui Fan, Yu-Chi Chen, Tonya Watkins, Chi V. Dang, Myriam Gorospe, and Chris Cheadle
34. In Vivo Run on Assays to Monitor Nascent Precursor RNA Transcripts
Piergiorgio Percipalle and Emilie Louvet
35. Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag Next Generation Sequencing (RNA-PET)
Xiaoan Ruan and Yijun Ruan
36. Analysis of Cotranscriptionnal RNA Processing by RNA-ChIP Assay
Danielle Bittencourt and Didier Auboeuf
37. Quantitative Analysis of Transcription Elongation by RNA Polymerase I In Vitro
David Alan Schneider
38. Detection and Characterization of Transcription Termination
Ghada Ghazal, Jules Gagnon, and Sherif Abou Elela
39. Promoter-Associated Noncoding RNA from the CCND1 Promoter
Xiaoyuan Song, Xiangting Wang, Shigeki Arai, and Riki Kurokawa
PRODUCT DETAILS
Publisher: Springer (Humana Press Inc.)
Publication date: November, 2011
Pages: 644
Weight: 1391g
Availability: Available
Subcategories: Biochemistry, Genetics
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