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Plant Gene Regulatory Networks

Overview of attention for book
Cover of 'Plant Gene Regulatory Networks'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants
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    Chapter 2 Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
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    Chapter 3 Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
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    Chapter 4 Characterization of Cell-Type-Specific DNA Binding Sites of Plant Transcription Factors Using Chromatin Immunoprecipitation
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    Chapter 5 Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries
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    Chapter 6 SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors
  8. Altmetric Badge
    Chapter 7 Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
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    Chapter 8 Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
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    Chapter 9 Characterization of Mediator Complex and its Associated Proteins from Rice
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    Chapter 10 DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
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    Chapter 11 In Situ Hi-C Library Preparation for Plants to Study Their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
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    Chapter 12 Multiplexed Transcriptional Activation or Repression in Plants Using CRISPR-dCas9-Based Systems
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    Chapter 13 Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants
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    Chapter 14 Design of Knowledge Bases for Plant Gene Regulatory Networks
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    Chapter 15 AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
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    Chapter 16 Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
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    Chapter 17 Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data
  19. Altmetric Badge
    Chapter 18 Computational Approaches to Study Gene Regulatory Networks
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    Chapter 19 Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction
  21. Altmetric Badge
    Chapter 20 ODE-Based Modeling of Complex Regulatory Circuits
  22. Altmetric Badge
    Chapter 21 Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach
Attention for Chapter 7: Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
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Chapter title
Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems
Chapter number 7
Book title
Plant Gene Regulatory Networks
Published in
Methods in molecular biology, June 2017
DOI 10.1007/978-1-4939-7125-1_7
Pubmed ID
Book ISBNs
978-1-4939-7124-4, 978-1-4939-7125-1
Authors

Díaz-Triviño, Sara, Long, Yuchen, Scheres, Ben, Blilou, Ikram, Sara Díaz-Triviño, Yuchen Long, Ben Scheres, Ikram Blilou

Editors

Kerstin Kaufmann, Bernd Mueller-Roeber

Abstract

In plant biology, transient expression systems have become valuable approaches used routinely to rapidly study protein expression, subcellular localization, protein-protein interactions, and transcriptional activity prior to in vivo studies. When studying transcriptional regulation, luciferase reporter assays offer a sensitive readout for assaying promoter behavior in response to different regulators or environmental contexts and to confirm and assess the functional relevance of predicted binding sites in target promoters. This chapter aims to provide detailed methods for using luciferase reporter system as a rapid, efficient, and versatile assay to analyze transcriptional regulation of target genes by transcriptional regulators. We describe a series of optimized transient expression systems consisting of Arabidopsis thaliana protoplasts, infiltrated Nicotiana benthamiana leaves, and human HeLa cells to study the transcriptional regulations of two well-characterized transcriptional regulators SCARECROW (SCR) and SHORT-ROOT (SHR) on one of their targets, CYCLIN D6 (CYCD6).Here, we illustrate similarities and differences in outcomes when using different systems. The plant-based systems revealed that the SCR-SHR complex enhances CYCD6 transcription, while analysis in HeLa cells showed that the complex is not sufficient to strongly induce CYCD6 transcription, suggesting that additional, plant-specific regulators are required for full activation. These results highlight the importance of the system and suggest that including heterologous systems, such as HeLa cells, can provide a more comprehensive analysis of a complex gene regulatory network.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 14 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 14 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 29%
Student > Doctoral Student 2 14%
Student > Bachelor 2 14%
Professor > Associate Professor 2 14%
Researcher 2 14%
Other 1 7%
Unknown 1 7%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 36%
Agricultural and Biological Sciences 5 36%
Engineering 2 14%
Pharmacology, Toxicology and Pharmaceutical Science 1 7%
Unknown 1 7%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 18 June 2017.
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#9,109,245
of 11,378,832 outputs
Outputs from Methods in molecular biology
#3,891
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Outputs of similar age
#191,439
of 264,773 outputs
Outputs of similar age from Methods in molecular biology
#8
of 11 outputs
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