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This second edition details protocols that analyze and explore gene regulatory networks (GRNs). Chapters guide readers through experimental techniques used to study genes and their regulatory interactions in plants, and computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.
Authoritative and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.
List of contents
Characterization of gene regulatory networks in plants using new methods and data types.- Inducible, tissue-specific gene expression in Arabidopsis using GR-LhG4-mediated trans-activation.- Targeted activation of Arabidopsis genes by a potent CRISPR-Act3.0 system.- Single cell RNA-sequencing in Arabidopsis root tissues.- Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry.- Untargeted proteomics and metabolomics analysis of plant organ development.- DamID-seq: A DNA methylation method that captures both transient and stable TF-DNA interactions genome-wide in plant cells.- CUT&Tag for mapping in vivo protein-DNA interactions in plants.- Identification of plant transcription factor DNA-binding sites using seq-DAP-seq.- Estimating DNA-binding specificities of transcription factors using SELEX-seq.- Immunoprecipitation-mass spectrometry (IP-MS) of protein-protein interactions of nucleus-localized plant proteins.- Mapping active gene modules by ChIA-PET in rice.- Building high-confidence gene regulatory networks by integrating validated TF-target gene interactions using ConnecTF.- The ChIP-hub resource: towards plantEncode.- A practical guide to inferring multi-omics networks in plant systems.- Gene regulatory network modelling using single-cell multi-omics in plants.- Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information.- Predicting gene regulatory interactions using natural genetic variation.- Prediction of transcription factor regulators and gene regulatory networks in tomato using binding site information.- AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis.- A transferable machine learning framework for predicting transcriptional responses of gene across species.
