Plant Transcription Factors: Methods and Protocols

ISBN-13: 9781617791536 / Angielski / Twarda / 2011 / 347 str.

Ling Yuan; Sharyn E. Perry

Opis

Recent years have seen significant advances in technologies that enable us to analyse transcription factors, a pivotal cell regulatory process in plants. This comprehensive survey covers the basic concepts as well as detailed protocols of tools to study transcription factors.

Recenzje

From the reviews:

"It represents a collection of protocols for performing analysis on plant transcription factors (TFs). ... this book will be very useful to many research groups. The different protocols are described in a user-friendly manner which makes it an excellent source of information for students and scientists that are new to the field. In addition, it is well suited to serve as a basis to optimize the broad array of techniques relevant to the field of plant transcription factor research." (Tzvetina Brumbarova, Journal of Plant Physiology, Vol. 169 (13), 2012)

Spis treści

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

 

 

 

 

 

 

 

           

Blurb

Recent years have seen significant advancements in the development of enabling technologies that facilitate the study of Transcription Factors (TFs). TFs are pivotal in the regulation of plant development, reproduction, intercellular signaling, response to environment, cell cycle, and metabolism. Plant Transcription Factors: Methods and Protocols offers a comprehensive approach by covering the basic concepts as well as the detailed protocols of a series of commonly used tools for investigating plant TFs. From discussing select TF families in plants to presenting approaches for identifying them, methods are covered to verify the function, to identify protein interactions in which TFs are involved, and how the interactions are mediated. Increasing examples of TFs that function non-cell-autonomously are being discovered and methods to assess intercellular trafficking are also addressed. A section is devoted to examining interaction with DNA, and the volume concludes with a discussion of directed evolution to generate transcription factors that can more efficiently control desired processes. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and accessible, Plant Transcription Factors: Methods and Protocols serves as an ideal guide to seasoned plant molecular biologists as well as scientists new to the field of TFs and provides many necessary methods to all scientists who are interested in exploring the functions of transcription factors.