Plant Gene Regulatory Networks

ISBN-13: 9781071633533 / Angielski / Twarda / 2023

Opis

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. 

Spis treści

1: Characterization of gene regulatory networks in plants using new methods and data types

K. Vandepoele and K. Kaufmann

 

2: Inducible, tissue-specific gene expression in Arabidopsis using GR-LhG4-mediated trans-activation

T. Zerin, T. Greb and S. Wolf

 

Targeted activation of Arabidopsis genes by a potent CRISPR–Act3.0 system

C. Pan and Y. Qi

 

4: Single cell RNA-sequencing in Arabidopsis root tissues

 Y. Ke, M. Minne, T. Eeckhout and B. De Rybel

 

5: Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry

K.W. Berendzen, C. Grefen, T. Sakamoto and D. Slane

 

6: Untargeted proteomics and metabolomics analysis of plant organ development

V. P. Thirumalaikumar, A.R. Fernie and A. Skirycz

 

7: DamID-seq: A DNA methylation method that captures both transient and stable TF-DNA interactions genome-wide in plant cells

J.M. Alvarez, W. Hinckley, L. Leonelli, M.D. Brooks and G.M. Coruzzi

 

8: CUT&Tag for mapping in vivo protein-DNA interactions in plants

W. Ouyang and X. Li

 

9: Identification of plant transcription factor DNA-binding sites using seq-DAP-seq

S. Hutin, R Blanc-Mathieu, P Rieu, F. Parcy, X. Lai and C. Zubieta

 

10: Estimating DNA-binding specificities of transcription factors using SELEX-seq

P. Chen, C. Smaczniak, J. Haffner, J.M. Muino and K. Kaufmann

 

11: Immunoprecipitation-mass spectrometry (IP-MS) of protein-protein interactions of nucleus-localized plant proteins

C. Smaczniak

 

12: Mapping active gene modules by ChIA-PET in rice

W. Ouyang and X. Li

 

13: Building high-confidence gene regulatory networks by integrating validated TF-target gene interactions using ConnecTF

J. Huang, M. S. Katari, C.-L. Juang, G.-M. Coruzzi, M.D. Brooks

 

14: The ChIP-hub resource: towards plantEncode

Y. Lan, X. Zhao and D. Chen

 

15: A practical guide to inferring multi-omics networks in plant systems

 N. M. Clark, B. Hurgobin, D.R. Kelley, M.G. Lewsey and J. W. Walley

 

16: Gene regulatory network modelling using single-cell multi-omics in plants

T. Chau, P. Timilsena and S. Li

 

17: Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information

H. N. Gavgani, E. Grotewold, J. Gray

 

18: Predicting gene regulatory interactions using natural genetic variation

M. John, D. Grimm and A. Korte

 

19: Prediction of transcription factor regulators and gene regulatory networks in tomato using binding site information

N. M. Perez and K. Vandepoele

 

20: AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis

V. Lau and N. J. Provart

 

21: A transferable machine learning framework for predicting transcriptional responses of gene across species

Z. Liang, X. Meng and J. C. Schnable