Plant Long Non-Coding RNAs: Methods and Protocols (Methods in Molecular Biology)

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Preface... Table of Contents... Contributing Authors... 1 An 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 2 Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis Todd Blevins, Ram Podicheti, and Craig S. Pikaard 3 Identification of Long Non-Coding RNAs in the Developing Endosperm of Maize Eundeok Kim, Yuqing Xiong, Byung-Ho Kang, and Sibum Sung 4 RNA 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 5 Improved Method of RNA Isolation from Laser Capture Microdissection (LCM) Derived-Plant Tissues Vibhav Gautam, Archita Singh, Sharmila Singh, Swati Verma, and Ananda K. Sarkar 6 Medium Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays Edith Francoz, Philippe Ranocha, Christophe Dun, and Vincent Burlat 7 Purification 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 8 The Involvement of Long Non-Coding RNAs in Response to Plant Stress Akihiro Matsui and Motoaki Seki 9 Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance Tao Qin and Liming Xiong 10 Discovery, 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 11 Bioinformatics 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 12 Identification of Novel lincRNA and Co-Expression Network Analysis using RNA Sequencing Data in Plants Song Qi, Shamima Akter, and Song Li 13 An Easy-to-Follow Pipeline for Long Non-Coding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca Chunying Kang and Zhongchi Liu 14 Reference-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 15 NAMS: Non-Coding Assessment in Magnoliophyta Species Gaurav Sablok, Kun Sun, and Hao Sun 16 De novo Plant Transcriptome 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 17 Identification 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 18 Analysis of Interaction between Long Non-Coding RNAs and Protein by RNA-Immunoprecipitation in Arabidopsis Jun Sung Seo and Nam-Hai Chua 19 Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants Jun Sung Seo and Nam-Hai Chua 20 In Vivo Genome-Wide RNA Structure Probing with Structure-seq2 Laura E. Ritchey, Zhao Su, Sarah M. Assmann, and Philip C. Bevilacqua 21 Using 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 22 Computationally 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 23 Stalking Structure in Plant Long Non-Coding RNAs Karissa Y. Sanbonmatsu 24 Transcriptome-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 25 A Walkthrough to the Use of GreeNC: The Plant lncRNA Database Andreu Paytuví, Walter Sanseverino, and Riccardo Aiese Cigliano 26 CANTATAdb 2.0: Expanding the Collection of Plant Long Non-Coding RNAs Michal Wojciech Szczesniak, Oleksii Bryzghalov, Joanna Ciomborowska-Basheer, and Izabela Makalowska 27 Experimentally 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 28 In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions Sudharsan Padmarasu, Axel Himmelbach, Martin Mascher, and Nils Stein