Section I. Introduction
1. MADS & More: Transcription Factors that Shape the Plant
Rainer Melzer and Günter Theißen
Section II. Identification of Transcription Factors
2. In Silico Mining and PCR Based Approaches to Transcription Factor Discovery in Non-Model Plants: Gene Discovery of the WRKY Transcription Factors in Conifers
Jun-Jun Liu and Yu Xiang
3. Isolation of Plant Transcription Factors Using a Yeast One-Hybrid System
Tatiana Pyvovarenko and Sergiy Lopato
4. A Transposon Based Activation Tagging System for Gene Function Discovery in Arabidopsis
Nayelli Marsch-Martínez
Section III. Functional Verification
5. CRES-T, An Effective Gene Silencing System Utilizing Chimeric Repressors
Nobutaka Mitsuda, Kyoko Matsui, Miho Ikeda, Masaru Nakata, Yoshimi Ooshima, Yukari Nagatoshi, and Masaru Ohme-Takagi
6. Analysis of a Transcription Factor Using Transient Assay in Arabidopsis Protoplasts
Yuji Iwata, Mi-Hyun Lee, and Nozomu Koizumi
7. Microarray-Based Identification of Transcription Factor Target Genes
Maartje Gorte, Anneke Horstman, Robert B. Page, Renze Heidstra, Arnold Stromberg, and Kim Boutilier
Section IV. Protein-Protein Interaction and Other Means for Activity Control
8. Yeast Protein-Protein Interaction Assays and Screens
Stefan de Folter and Richard G.H. Immink
9. Mapping Functional Domains of transcription factors
Ling Zhu and Enamul Huq
10. Bimolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts
Sitakanta Pattanaik, Joshua R. Werkman, and Ling Yuan
11. Isolation of transcription factor complexes from Arabidopsis cell suspension cultures by tandem affinity purification
Jelle Van Leene, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Jan Geerinck, Gert Van Isterdael, Erwin Witters, and Geert De Jaeger
12. Assaying Transcription Factor Stability
Jasmina Kurepa and Jan A. Smalle
13. How to assess the intercellular trafficking of transcription factors
Munawar Ahmad, Won Kyong Cho, Yeonggil Rim, Lijun Huang, and Jae-Yean Kim
Section V. Protein-DNA Interaction
14. SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space
Chenglin Chai, Zidian Xie, and Erich Grotewold
15. Footprinting and Missing Nucleoside Analysis of Transcription Factor-DNA Complexes
Ivana L. Viola and Daniel H. Gonzalez
16. Chromatin immunoprecipitation to verify or to identify In Vivo protein-DNA interactions
Yumei Zheng and Sharyn E. Perry
17. Visualizing and characterizing In Vivo DNA-Binding Events and Direct Target Genes of Plant Transcription Factors
Jose M. Muiño, Gerco C. Angenent, and Kerstin Kaufmann
18. Mapping In Vivo Protein-DNA Interactions in Plants by DamID, a DNA Adenine Methylation-Based Method
Sophie Germann and Valérie Gaudin
Section VI. Engineering Metablolic Pathways using Transcription Factors
19. Directed Evolution through DNA Shuffling for the Improvement and Understanding of Genes and Promoters
Joshua R. Werkman, Sitakanta Pattanaik, and Ling Yuan
