Transcriptional Regulation

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 Sá-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-López, 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... Mehr