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