Plant Functional Genomics: Methods and Protocols

ISBN-13: 9781493949137 / Angielski / Miękka / 2016 / 532 str.

Jose M. Alonso; Anna N. Stepanova

Spis treści

Part I Epigenetics

 1. Epigenome Profiling of Specific Plant Cell Types Using a Streamlined INTACT Protocol and ChIP-seq
Roger B. Deal and Dongxue Wang

2. Whole-Genome DNA Methylation Profiling with Nucleotide Resolution
Tzung-Fu Hsieh

3. High-Throughput Nuclease-Mediated Probing of RNA Secondary Structure in Plant Transcriptomes
Lee E. Vandivier, Fan Li, and Brian D. Gregory

4. Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants
Wenli Zhang and Jiming Jiang

Part II Transcriptional, Translational, and Metabolic Analysis

5. Characterization of in-vivo DNA-Binding Events of Plant Transcription Factors by ChIP-seq: Experimental Protocol and Computational Analysis
Hilda van Mourik, Jose M. Muiño, Alice Pajoro, Gerco C. Angenent, and Kerstin Kaufmann

6. Identification of Direct Targets of Plant Transcription Factors Using the GR Fusion TechniqueNobutoshi Yamaguchi, Cara M. Winter, Frank Wellmer, and Doris Wagner

7. Ribosome Profiling: A Tool for Quantitative Evaluation of Dynamics in mRNA Translation
Piyada Juntawong, Maureen Hummel, Jeremie Bazin, and Julia Bailey-Serres

8. Tissue-Specific Gene Expression Profiling by Cell Sorting
Pui-Leng Ip and Kenneth D. Birnbaum

9. Translating Ribosome Affinity Purification (TRAP) Followed by RNA Sequencing Technology (TRAP-SEQ) for Quantitative Assessment of Plant Translatomes
Mauricio A. Reynoso, Piyada Juntawong, Marcos Lancia, Flavio A. Blanco, Julia Bailey-Serres, and María Eugenia Zanetti

10. Rapid Immunopurification of Ribonucleoprotein Complexes of Plants
Reed Sorenson and Julia Bailey-Serres

11. Metabolomic Profiling of Plant Tissues
José L. Rambla, M. P. López-Gresa, J. M. Bellés, and Antonio Granell

Part III Forward and Reverse Genetics

12. Targeted Plant Genome Editing via the CRISPR/Cas9 Technology
Jian-Feng Li, Dandan Zhang, and Jen Sheen

13. QTL Mapping Using High-Throughput Sequencing
Tiffany M. Jamann, Peter J. Balint-Kurti, and James B. Holland

14. Quantitating Plant MicroRNA-Mediated Target Repression Using a Dual-Luciferase Transient Expression System
Qikun Liu and Michael J. Axtell

15. Persistent Virus-Induced Gene Silencing in Asymptomatic Accessions of Arabidopsis
Miguel A. Flores, Maria I. Reyes, Dominique Robertson, and Susanne Kjemtrup

16. A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections
Ronan C. O'Malley, Cesar C. Barragan, and Joseph R. Ecker

17. Genome-Wide Association Mapping in Plants Exemplified for Root Growth in Arabidopsis thaliana
Radka Slovak, Christian Göschl, Ümit Seren, and Wolfgang Busch

18. Tilling By Sequencing
Helen Tsai, Kathie Ngo, Meric Lieberman, Victor Missirian, and Luca Comai

19. SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens
Hequan Sun and Korbinian Schneeberger

Part IV Tools to Accelerate Gene Functional Analysis and Plant Synthetic Biology

20. Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework
Marta Vazquez-Vilar , Alejandro Sarrion-Perdigones, Peio Ziarsolo, Jose Blanca, Antonio Granell, and Diego Orzaez

21. Ligation Independent Cloning for Plant Research
Jos R. Wendrich, Che-Yang Liao, Willy A. M. van den Berg, Bert De Rybel, and Dolf Weijers

22. Gene Functional Analysis Using Protoplast Transient Assays
Ha-il Jung, Jiapei Yan, Zhiyang Zhai, and Olena K. Vatamaniuk

Part V Computational Approaches to Functional Genomics

23. Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era
Jose Davila-Velderrain, Juan C. Martinez-Garcia, Elena R. Alvarez- Buylla

24. Analysis and Visualization of RNA-Seq Expression Data Using RStudio, Bioconductor, and Integrated Genome Browser
Ann E. Loraine, Ivory Clabaugh Blakley, Sridharan Jagadeesan, Jeff Harper, Gad Miller, Nurit Firon

25. Constructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants
Tomás C. Moyano, Elena A. Vidal, Orlando Contreras-López, and Rodrigo A. Gutiérrez

Blurb

This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utilized by a wide array of plant biologists to address specific questions in their favorite model systems. This book is organized into five parts. Part I examines the tools and methods required for identifying epigenetic and conformational changes at the whole-genome level. Part II presents approaches used to determine key aspects of a gene’s function, such as techniques used to identify and characterize gene regulatory networks. This is followed by a discussion of tools used to analyze the levels of mRNA, mRNA translation rates, and metabolites. Part III features a compilation of forward and reverse genetic approaches that include recent implementation of high-throughput sequencing in classical methodologies such as QTL mapping. The final two parts explore strategies to facilitate and accelerate the generation and testing of functional DNA elements, and basic computational tools used to facilitate the use of systems biology approached by a broad spectrum of plant researchers. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.

Practical and timely, Plant Functional Genomics: Methods and Protocols, Second Edition highlights the latest developments in DNA sequencing technologies that are likely to continue shaping the future of functional genomics.