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 volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. Written in the highly successful Methods in 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 tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.
Preface...
Table of Contents...
Contributing Authors...
1An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!
Hsiao-Lin V. Wang and Julia A. Chekanova
Part I Role of ncRNAs in Regulation of Gene Expression and Development in Plants
2Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis
Todd Blevins, Ram Podicheti, and Craig S. Pikaard
3Identification of Long Non-Coding RNAs in the Developing Endosperm of Maize
Eundeok Kim, Yuqing Xiong, Byung-Ho Kang, and Sibum Sung
4RNA Isolation and Analysis of lncRNAs from Gametophytes of Maize
Linqian Han, Lin Li, Gary J. Muehlbauer, John E. Fowler, and Matthew M. S. Evans
Part II Studying the Tissue and Cell-Type Specific lncRNAs
5Improved Method of RNA Isolation from Laser Capture Microdissection (LCM) Derived-Plant Tissues
Vibhav Gautam, Archita Singh, Sharmila Singh, Swati Verma, and Ananda K. Sarkar
6Medium Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays
Edith Francoz, Philippe Ranocha, Christophe Dun, and Vincent Burlat
7Purification and Functional Analysis of Plant Long Non-Coding RNAs (lncRNA)
Trung Do, Zhipeng Qu, and Iain Searle
Part III Studying lncRNAs Associated with Response to Abiotic and Biotic Stresses in Plants
8The Involvement of Long Non-Coding RNAs in Response to Plant Stress
Akihiro Matsui and Motoaki Seki
9Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance
Tao Qin and Liming Xiong
10Discovery, Identification, and Functional Characterization of Plant Long Intergenic Non-Coding RNAs after Virus Infection
Ruimin Gao, Peng Liu, Nadia Irwanto, De Rong Loh, and Sek-Man Wong
Part IV Identification and Functional Analysis of lncRNAs
11Bioinformatics Approaches to Studying Plant Long Non-Coding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-seq Data Sets
Hai-Xi Sun and Nam-Hai Chua
12Identification of Novel lincRNA and Co-Expression Network Analysis using RNA Sequencing Data in Plants
Song Qi, Shamima Akter, and Song Li
13An Easy-to-Follow Pipeline for Long Non-Coding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca
Chunying Kang and Zhongchi Liu
14Reference-Based Identification of Long Non-Coding RNAs in Plants with Strand-Specific RNA-Sequencing Data
Xiao Lin, Meng Ni, Zhixia Xiao, Ting-Fung Chan, and Hon-Ming Lam
15NAMS: Non-Coding Assessment in Magnoliophyta Species
Gaurav Sablok, Kun Sun, and Hao Sun
16De novo Plant Tranillegalscriptome Assembly and Annotation using Illumina RNA-seq Reads
Stephanie C. Kerr, Federico Gaiti, and Milos Tanurdzic
Part V Purification of lncRNAs and Ribonucleoprotein Complexes, RNA Secondary Structure, and RNA Modifications
17Identification of Long Non-Coding RNA-Protein Interactions through In Vitro RNA Pull-Down Assay with Plant Nuclear Extracts
Jun Sung Seo and Nam-Hai Chua
18Analysis of Interaction between Long Non-Coding RNAs and Protein by RNA-Immunoprecipitation in Arabidopsis
Jun Sung Seo and Nam-Hai Chua
19Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants
Jun Sung Seo and Nam-Hai Chua
20In Vivo Genome-Wide RNA Structure Probing with Structure-seq2
Laura E. Ritchey, Zhao Su, Sarah M. Assmann, and Philip C. Bevilacqua
21Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Non-Coding RNAs in Plants
Marianne C. Kramer and Brian D. Gregory
22Computationally Characterizing Protein Bound Long Non-Coding RNAs and their Secondary Structure using Protein Interaction Profile Sequencing (PIP-seq) in Plants
Mengge Shan, Zachary D. Anderson, and Brian D. Gregory
23Stalking Structure in Plant Long Non-Coding RNAs
Karissa Y. Sanbonmatsu
24Tranillegalscriptome-Wide Mapping 5-methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant
Xiaofeng Gu and Zhe Liang
Part VI Databases of Plant lncRNAs and How to Use Them
25A Walkthrough to the Use of GreeNC: The Plant lncRNA Database
Andreu Paytuví, Walter Sanseverino, and Riccardo Aiese Cigliano
26CANTATAdb 2.0: Expanding the Collection of Plant Long Non-Coding RNAs
Michal Wojciech Szczesniak, Oleksii Bryzghalov, Joanna Ciomborowska-Basheer, and Izabela Makalowska
27Experimentally Validated Plant lncRNAs in EVLncRNAs Database
Bailing Zhou, Huiying Zhao, Jiafeng Yu, Chengang Guo, Xianghua Dou, Feng Song, Guodong Hu, Zanxia Cao, Yuanxu Qu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
Part VII Long-Range Chromatin Interactions and Chromosome Conformation Capture
28In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions
Sudharsan Padmarasu, Axel Himmelbach, Martin Mascher, and Nils Stein
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!.- Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis.- Identification of Long Non-Coding RNAs in the Developing Endosperm of Maize.- RNA Isolation and Analysis of lncRNAs from Gametophytes of Maize.- Improved Method of RNA Isolation from Laser Capture Microdissection (LCM) Derived-Plant Tissues.- Medium Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays.- Purification and Functional Analysis of Plant Long Non-Coding RNAs (lncRNA).- The Involvement of Long Non-Coding RNAs in Response to Plant Stress.- Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance.- Discovery, Identification, and Functional Characterization of Plant Long Intergenic Non-Coding RNAs after Virus Infection.- Bioinformatics Approachesto Studying Plant Long Non-Coding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-seq Data Sets.- Identification of Novel lincRNA and Co-Expression Network Analysis using RNA Sequencing Data in Plants.- An Easy-to-Follow Pipeline for Long Non-Coding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca.- Reference-Based Identification of Long Non-Coding RNAs in Plants with Strand-Specific RNA-Sequencing Data.- NAMS: Non-Coding Assessment in Magnoliophyta Species.- De novo Plant Tranillegalscriptome Assembly and Annotation using Illumina RNA-seq Reads.- Identification of Long Non-Coding RNA-Protein Interactions through In Vitro RNA Pull-Down Assay with Plant Nuclear Extracts.- Analysis of Interaction between Long Non-Coding RNAs and Protein by RNA-Immunoprecipitation in Arabidopsis.- Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants.- In Vivo Genome-Wide RNA Structure Probing with Structure-seq2.- Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Non-Coding RNAs in Plants.- Computationally Characterizing Protein Bound Long Non-Coding RNAs and their Secondary Structure using Protein Interaction Profile Sequencing (PIP-seq) in Plants.- Stalking Structure in Plant Long Non-Coding RNAs.- Tranillegalscriptome-Wide Mapping 5-methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant.- A Walkthrough to the Use of GreeNC: The Plant lncRNA Database.- CANTATAdb 2.0: Expanding the Collection of Plant Long Non-Coding RNAs.- Experimentally Validated Plant lncRNAs in EVLncRNAs Database.- In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions.
Inhaltsverzeichnis
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!.- Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis.- Identification of Long Non-Coding RNAs in the Developing Endosperm of Maize.- RNA Isolation and Analysis of lncRNAs from Gametophytes of Maize.- Improved Method of RNA Isolation from Laser Capture Microdissection (LCM) Derived-Plant Tissues.- Medium Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays.- Purification and Functional Analysis of Plant Long Non-Coding RNAs (lncRNA).- The Involvement of Long Non-Coding RNAs in Response to Plant Stress.- Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance.- Discovery, Identification, and Functional Characterization of Plant Long Intergenic Non-Coding RNAs after Virus Infection.- Bioinformatics Approachesto Studying Plant Long Non-Coding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-seq Data Sets.- Identification of Novel lincRNA and Co-Expression Network Analysis using RNA Sequencing Data in Plants.- An Easy-to-Follow Pipeline for Long Non-Coding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca.- Reference-Based Identification of Long Non-Coding RNAs in Plants with Strand-Specific RNA-Sequencing Data.- NAMS: Non-Coding Assessment in Magnoliophyta Species.- De novo Plant Tranillegalscriptome Assembly and Annotation using Illumina RNA-seq Reads.- Identification of Long Non-Coding RNA-Protein Interactions through In Vitro RNA Pull-Down Assay with Plant Nuclear Extracts.- Analysis of Interaction between Long Non-Coding RNAs and Protein by RNA-Immunoprecipitation in Arabidopsis.- Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants.- In Vivo Genome-Wide RNA Structure Probing with Structure-seq2.- Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA-Protein Interaction Sites of Long Non-Coding RNAs in Plants.- Computationally Characterizing Protein Bound Long Non-Coding RNAs and their Secondary Structure using Protein Interaction Profile Sequencing (PIP-seq) in Plants.- Stalking Structure in Plant Long Non-Coding RNAs.- Tranillegalscriptome-Wide Mapping 5-methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant.- A Walkthrough to the Use of GreeNC: The Plant lncRNA Database.- CANTATAdb 2.0: Expanding the Collection of Plant Long Non-Coding RNAs.- Experimentally Validated Plant lncRNAs in EVLncRNAs Database.- In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions.
Klappentext
This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. Written in the highly successful Methods in 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 tips on troubleshooting and avoiding known pitfalls.nnCutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
