Plant Gene Regulatory Networks: Methods and Protocols

by Kerstin Kaufmann (Editor), Bernd Mueller-Roeber (Editor)

Overview

This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana. 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.

Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.

Product Details

ISBN-13:	9781493983926
Publisher:	Springer New York
Publication date:	08/08/2018
Series:	Methods in Molecular Biology , #1629
Edition description:	Softcover reprint of the original 1st ed. 2017
Pages:	350
Product dimensions:	7.01(w) x 10.00(h) x (d)

Table 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.