Plant Transcription Factors: Methods and Protocols

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

            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

            Ren Li and Xia Cui

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

            Xiuli Bi and Chang Liu