Plant Transcription Factors

Description

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. Front Matter ....Pages i-xii Front Matter ....Pages 1-1 Master Regulatory Transcription Factors in Plant Development: A Blooming Perspective (Kerstin Kaufmann, Chiara A. Airoldi)....Pages 3-22 Application of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants (Felix Wolter, Holger Puchta)....Pages 23-40 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, Jiro Sugisaka)....Pages 41-57 Front Matter ....Pages 59-59 Generation of Inducible Transgenic Lines of Arabidopsis Transcription Factors Regulated by MicroRNAs (Pooja Aggarwal, Krishna Reddy Challa, Monalisha Rath, Preethi Sunkara, Utpal Nath)....Pages 61-79 A Specific Knockdown of Transcription Factor Activities in Arabidopsis (Beibei Zheng, Bennett Thomson, Frank Wellmer)....Pages 81-92 Using CRISPR/Cas9 System to Introduce Targeted Mutation in Arabidopsis (Ze Hong Lee, Nobutoshi Yamaguchi, Toshiro Ito)....Pages 93-108 CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha (Shigeo S. Sugano, Ryuichi Nishihama)....Pages 109-126 Cell-Type-Specific Promoter Identification Using Enhancer Trap Lines (Tatyana Radoeva, Shunsuke Saiga, Dolf Weijers)....Pages 127-139 Isolation of Arabidopsis Palisade and Spongy Mesophyll Cells (Kyohei Uemoto, Takashi Araki, Motomu Endo)....Pages 141-148 Ectopic Vascular Induction in Arabidopsis Cotyledons for Sequential Analysis of Phloem Differentiation (Alif Meem Nurani, Yuki Kondo, Hiroo Fukuda)....Pages 149-159 Front Matter ....Pages 161-161 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, Ken Shirasu)....Pages 163-189 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, Pascal Gamas)....Pages 191-224 NanoCAGE-XL: An Approach to High-Confidence Transcription Start Site Sequencing (Maria G. Ivanchenko, Molly Megraw)....Pages 225-237 Genome-Wide TSS Identification in Maize (María Katherine Mejia-Guerra, Wei Li, Andrea I. Doseff, Erich Grotewold)....Pages 239-256 Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee (Yoko Mizuta, Katsutoshi Tsuda)....Pages 257-268 Two-Color In Situ Hybridization: A Technique for Simultaneous Detection of Transcripts from Different Loci (Taiyo Toriba, Hiro-Yuki Hirano)....Pages 269-287 Front Matter ....Pages 289-289 Gene Expression and Transcription Factor Binding Tests Using Mutated-Promoter Reporter Lines (Ayako Nishizawa-Yokoi, Nobutoshi Yamaguchi)....Pages 291-305 Rapid and Quantitative CELD Assay to Measure the Specificity of Transcription Factor-DNA-Binding Interactions and Identify cis-Elements (Sundaravelpandian Kalaipandian, Gang-Ping Xue)....Pages 307-324 In Situ Proximity Ligation Assay to Detect the Interaction Between Plant Transcription Factors and Other Regulatory Proteins (Yifeng Xu, Eng-Seng Gan, Toshiro Ito)....Pages 325-335 Cell-Free Protein Synthesis of Plant Transcription Factors (Mika Nomoto, Yasuomi Tada)....Pages 337-349 Front Matter ....Pages 351-351 Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants (Wenli Zhang, Jiming Jiang)....Pages 353-366 Genome-Wide Mapping of DNase I Hypersensitive Sites in Tomato (Ren Li, Xia Cui)....Pages 367-379 Genome-Wide Identification of Chromatin Domains Anchored at the Nuclear Periphery in Plants (Xiuli Bi, Chang Liu)....Pages 381-393 Back Matter ....Pages 395-396