Plant Transcription Factors

This volume discusses the latest advancements in the study of plant transcription factors (TFs), and includes discussions on experimental setups, analytical pipelines, and examples on how to optimize information from databases and resources related to plant TFs. The chapters in this book are organized into three parts. Part One covers high-throughput methodologies for identifying TF binding sites. This part includes standardized and optimized protocols for DAP-seq, ChIP-seq, and CUT&Tag. Part Two centers on the visualization and quantification TF-DNA and TF-protein interactions. This section talks about methodologies used to investigate the localization and timing of transcriptional complex formation in vivo. Part Three explores the integrative frameworks that combine transcriptomics with binding site prediction and gene regulatory networks inference tools. Written in the highly successful Methods in Molecular Biology series format, 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.

Cutting-edge and thorough, Plant Transcription Factors: Methods and Protocols is a valuable resource for researchers and laboratories focused on learning more about this important and advancing field.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt

Standardized Protocols and Bioinformatic Pipelines for Conducting DAP-Seq Experiments in Non-Model Plant Crops.- Chromatin Immunoprecipitation in Crops.- Cleavage Under Targets and Tagmentation (CUT&Tag) Protocol for Plants.- Identification of Accessible Transcription Factor Binding Sites During the Seed-To-Seedling Transition.- Dual Luciferase Assay System for Quantification of Promoter Activity.- Yeast One-Hybrid (Y1H) Assay for Single Promoter-Transcription Factor Interaction in Higher Plants.- Targeted DNA Affinity Purification for Quantifying DNA-Binding Specificities of Transcription Factors.- The Yeast Two-Hybrid System: In Vivo * Detection of Direct Protein-Protein Interactions.- Identification of Protein-Protein Interactions in Strawberry Fruit Using Immunoprecipitation-Mass Spectrometry (IP-MS) Assay.- TurboID-Based Proximity Labelling in Plants.- FRET-FLIM: Unveiling Transcription Factor Interactions in Plants.- MINI-EX Version 2: Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell Transcriptomics Approach.- A Practical Guide to Gene Regulatory Networks in Plants: From RNA Sequencing to Identification of Transcription Factor Binding Sites.- Web-Based Discovery of Regulatory Motifs in Non-Model Plants.- Inferring Gene Networks from High-Throughput Transcriptomes.- Comparative Genomics using GeneDiscoveR: A Toolbox* for Identification of Gene Candidates Associated to Plant Traits.