Plant Gene Regulatory Networks: Methods and Protocols

Preface...
Table of Contents...

Contributing Authors...

1. From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants

Kerstin Kaufmann and Dijun Chen

Part I Experimental Approaches to Study Plant Gene-Regulatory Networks

2. Inducible Promoter Systems for Gene Perturbation Experiments in Arabidopsis
Bennett Thomson, Emmanuelle Graciet, and Frank Wellmer

3. Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
Daniel Slane and Martin Bayer

4. Characterization of Cell Type-Specific DNA Binding Sites of Plant Transcription Factors using Chromatin Immunoprecipitation
On Sun Lau

5. Yeast One and Two Hybrid High-Throughput Screenings using Arrayed Libraries
Rocío Sánchez-Montesino and Luis Oñate-Sánchez

6. SELEX-Seq: A Method to Determine DNA-Binding Specificities of Plant Transcription Factors
Cezary Smaczniak, Gerco C. Angenent and Kerstin Kaufmann

7. Analysis of a Plant Transcriptional Regulatory Network using Transient Expression Systems
Sara Díaz-Triviño, Yuchen Long, Ben Scheres, and Ikram Blilou

8. Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors
Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, and Klaus D. Grasser

9. Characterization of Mediator Complex and its Associated Proteins from Rice
Subhasis Samanta and Jitendra Kumar Thakur

10. DNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing
Sergei A. Filichkin and Molly Megraw

11. In Situ Hi-C Library Preparation for Plants to Study their Three-Dimensional Chromatin Interactions on a Genome-Wide Scale
Chang Liu

12. Multiplexed Transcriptional Activation or Repression in Plants using CRISPR-dCas9 Based Systems
Levi G. Lowder, Joseph W. Paul III, and Yiping Qi

13. Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants
Tom Schreiber and Alain Tissier

Part II Computational Approaches to Study Plant Gene-Regulatory Networks

14. Design of Knowledge Bases for Plant Gene Regulatory Networks
Eric Mukundi, Fabio Gomez-Cano, Wilberforce Zachary Ouma, and Erich Grotewold

15. AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species
Tak Lee and Insuk Lee

16. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development
Dijun Chen and Kerstin Kaufmann

17. Predicting Transcription Factor-Binding Sites and their Cognate Transcription Factors using Gene Expression Data
Chun-Ping Yu and Wen-Hsiung Li

18. Computational Approaches to Study Gene Regulatory Networks
Nooshin Omranian and Zoran Nikoloski

19. Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation and Prediction
J. Davila-Velderrain, J.C. Martinez-Garcia, and R.E. Alvarez Buylla

20. ODE-Based Modeling of Complex Regulatory Circuits
Daniel D. Seaton

21. Inferring Gene Regulatory Networks in the Arabidopsis Root using a Dynamic Bayesian Network Approach
Maria Angels de Luis Balaguer and Rosangela Sozzani