Plant Transcription Factors: Methods and Protocols

ISBN-13: 9781493986569 / Angielski / Twarda / 2018 / 396 str.

Nobutoshi Yamaguchi

Spis treści

Part I: Review and Overview Chapters

 

1. Master Regulatory Transcription Factors in Plant Development: A Blooming Perspective

            Kerstin Kaufmann and Chiara A. Airoldi

 

2. Application of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants

            Felix Wolter and Holger Puchta

 

3. The Long-Term ‘In Natura’ Study Sites of Arabidopsis halleri for Plant Transcription and Epigenetic Modification Analyses in Natural Environments

            Hiroshi Kudoh, Mie N. Honjo, Haruki Nishio, and Jiro Sugisaka

 

Part II: Preparation of Plant Materials

 

4. Generation of Inducible Transgenic Lines of Arabidopsis Transcription Factors Regulated by MicroRNAs

            Pooja Aggarwal, Krishna Reddy Challa, Monalisha Rath, Preethi Sunkara, and Utpal Nath

 

5. A Specific Knockdown of Transcription Factor Activities in Arabidopsis

            Beibei Zheng, Bennett Thomson, and Frank Wellmer

 

6. Using CRISPR/Cas9 System to Introduce Targeted Mutation in Arabidopsis

            Ze Hong Lee, Nobutoshi Yamaguchi, and Toshiro Ito

 

7. CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha

            Shigeo S. Sugano and Ryuichi Nishihama

 

8. Cell-Type-Specific Promoter Identification Using Enhancer Trap Lines

            Tatyana Radoeva, Shunsuke Saiga, and Dolf Weijers

 

9. Isolation of Arabidopsis Palisade and Spongy Mesophyll Cells

            Kyohei Uemoto, Takashi Araki, and Motomu Endo

 

10. Ectopic Vascular Induction in Arabidopsis Cotyledons for Sequential Analysis of Phloem Differentiation

            Alif Meem Nurani, Yuki Kondo, and Hiroo Fukuda

 

Part III: Detection of Expression Levels

 

11. High Impact Gene Discovery: Simple Strand Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-Expression Network

            Yasunori Ichihashi, Atsushi Fukushima, Arisa Shibata, and Ken Shirasu

 

12. Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti

            Brice Roux, Nathalie Rodde, Sandra Moreau, Marie-Françoise Jardinaud, and Pascal Gamas

 

13. nanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing

            Maria G. Ivanchenko and Molly Megraw

 

14. Genome-Wide TSS Identification in Maize

            María Katherine Mejia-Guerra, Wei Li, Andrea I. Doseff, and Erich Grotewold

 

15. Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee

            Yoko Mizuta and Katsutoshi Tsuda

 

16. Two-Color In Situ Hybridization: A Technique for Simultaneous Detection of Transcripts from Different Loci

            Taiyo Toriba and Hiro-Yuki Hirano

 

Part IV: Interaction Tests

 

17. Gene Expression and Transcription Factor Binding Tests Using Mutated-Promoter Reporter Lines

            Ayako Nishizawa-Yokoi and Nobutoshi Yamaguchi

 

18. Rapid and Quantitative CELD Assay to Measure the Specificity of Transcription Factor-DNA Binding Interactions and Identify cis-Elements

            Sundaravelpandian Kalaipandian and Gang-Ping Xue

 

19. In Situ Proximity Ligation Assay to Detect the Interaction between Plant Transcription Factors and Other Regulatory Proteins

            Yifeng Xu, Eng-Seng Gan, and Toshiro Ito

 

20. Cell-Free Protein Synthesis of Plant Transcription Factors

            Mika Nomoto and Yasuomi Tada

 

Part V: Chromation Analyses

 

21. Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants

            Wenli Zhang and Jiming Jiang

 

22. Genome-Wide Mapping of DNase I Hypersensitive Sites in Tomato

            Ren Li and Xia Cui

 

23. Genome-Wide Identification of Chromatin Domains Anchored at the Nuclear Periphery in Plants

            Xiuli Bi and Chang Liu

Blurb

This detailed book provides general protocols and technologies that plant biologists worldwide often utilize for the purpose of accelerating research progress in the field of plant transcription factors. Beginning with a brief introduction, the volume continues by exploring methods in the preparation of plant materials, detection of expression levels, interaction tests, and chromatin analyses. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Plant Transcription Factors: Methods and Protocols aims to answer a wide range of questions related to transcription factors commonly raised by plant biologists.