Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
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.
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 Tranillegalscriptomes
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 Tranillegalscriptional, Translational, and Metabolic Analysis
5. Characterization of in-vivo DNA-Binding Events of Plant Tranillegalscription 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 Tranillegalscription 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 Weijers22. 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. Deillegalscriptive 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
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.
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.
Epigenome Profiling of Specific Plant Cell Types Using a Streamlined INTACT Protocol and ChIP-seq.- Whole-Genome DNA Methylation Profiling with Nucleotide Resolution.- High-Throughput Nuclease-Mediated Probing of RNA Secondary Structure in Plant Tranillegalscriptomes.- Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants.- Characterization of in-vivo DNA-Binding Events of Plant Tranillegalscription Factors by ChIP-seq: Experimental Protocol and Computational Analysis.- Identification of Direct Targets of Plant Tranillegalscription Factors Using the GR Fusion Technique.- Ribosome Profiling: A Tool for Quantitative Evaluation of Dynamics in mRNA Translation.- Tissue-Specific Gene Expression Profiling by Cell Sorting.- Translating Ribosome Affinity Purification (TRAP) Followed by RNA Sequencing Technology (TRAP-SEQ) for Quantitative Assessment of Plant Translatomes.- Rapid Immunopurification of Ribonucleoprotein Complexes of Plants.- Metabolomic Profiling of Plant Tissues.- Targeted Plant Genome Editing via the CRISPR/Cas9 Technology.- QTL Mapping Using High-Throughput Sequencing.- Quantitating Plant MicroRNA-Mediated Target Repression Using a Dual-Luciferase Transient Expression System.- Persistent Virus-Induced Gene Silencing in Asymptomatic Accessions of Arabidopsis.- A User's Guide to the Arabidopsis T-DNA Insertion Mutant Collections.- Genome-Wide Association Mapping in Plants Exemplified for Root Growth in Arabidopsis thaliana.- Tilling By Sequencing.- SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens.- Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework.- Ligation Independent Cloning for Plant Research.- Gene Functional Analysis Using Protoplast Transient Assays.- Deillegalscriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era.- Analysis and Visualization of RNA-Seq Expression Data Using RStudio, Bioconductor, and Integrated Genome Browser.-Constructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants.
Inhaltsverzeichnis
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 Tranillegalscriptomes
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 Tranillegalscriptional, Translational, and Metabolic Analysis
5. Characterization of in-vivo DNA-Binding Events of Plant Tranillegalscription 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 Tranillegalscription 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. Deillegalscriptive 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
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
