CiNii Books - Plant functional genomics : methods and protocols

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.

Table of Contents

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. Muino, 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 Maria Eugenia Zanetti 10. Rapid Immunopurification of Ribonucleoprotein Complexes of Plants Reed Sorenson and Julia Bailey-Serres 11. Metabolomic Profiling of Plant Tissues Jose L. Rambla, M. P. Lopez-Gresa, J. M. Belles, 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 Goeschl, UEmit 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 Tomas C. Moyano, Elena A. Vidal, Orlando Contreras-Lopez, and Rodrigo A. Gutierrez

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Plant functional genomics : methods and protocols

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