Plant Gene Regulatory Networks : Methods and Protocols / edited by Kerstin Kaufmann, Klaas Vandepoele.

Format:

Book

Contributor:

Kaufmann, Kerstin, Editor.

Vandepoele, Klaas, Editor.

Series:

Methods in Molecular Biology, 1940-6029 ; 2698

Language:

English

Subjects (All):

Botany.

Plant genetics.

Plant Science.

Plant Genetics.

Local Subjects:

Plant Science.

Plant Genetics.

Physical Description:

1 online resource (XII, 382 p. 69 illus., 63 illus. in color.)

Edition:

2nd ed. 2023.

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2023.

Summary:

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. .

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.

ISBN:

9781071633540

1071633546