Plant Long Non-Coding RNAs: Methods and Protocols

✍ Scribed by Julia A. Chekanova, Hsiao-Lin V. Wang

• Publisher: Springer New York; Humana
• Year: 2019
• Tongue: English
• Leaves: 473
• Series: Methods in Molecular Biology 1933
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xvii
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK! (Hsiao-Lin V. Wang, Julia A. Chekanova)....Pages 1-30
Front Matter ....Pages 31-31
Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis (Todd Blevins, Ram Podicheti, Craig S. Pikaard)....Pages 33-48
Identification of Long Noncoding RNAs in the Developing Endosperm of Maize (Eundeok Kim, Yuqing Xiong, Byung-Ho Kang, Sibum Sung)....Pages 49-65
RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize (Linqian Han, Lin Li, Gary J. Muehlbauer, John E. Fowler, Matthew M. S. Evans)....Pages 67-86
Front Matter ....Pages 87-87
Improved Method of RNA Isolation from Laser Capture Microdissection (LCM)-Derived Plant Tissues (Vibhav Gautam, Archita Singh, Sharmila Singh, Swati Verma, Ananda K. Sarkar)....Pages 89-98
Medium-Throughput RNA In Situ Hybridization of Serial Sections from Paraffin-Embedded Tissue Microarrays (Edith Francoz, Philippe Ranocha, Christophe Dunand, Vincent Burlat)....Pages 99-130
Purification and Functional Analysis of Plant Long Noncoding RNAs (lncRNA) (Trung Do, Zhipeng Qu, Iain Searle)....Pages 131-147
Front Matter ....Pages 149-149
The Involvement of Long Noncoding RNAs in Response to Plant Stress (Akihiro Matsui, Motoaki Seki)....Pages 151-171
Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance (Tao Qin, Liming Xiong)....Pages 173-186
Discovery, Identification, and Functional Characterization of Plant Long Intergenic Noncoding RNAs After Virus Infection (Ruimin Gao, Peng Liu, Nadia Irwanto, De Rong Loh, Sek-Man Wong)....Pages 187-194
Front Matter ....Pages 195-195
Bioinformatics Approaches to Studying Plant Long Noncoding RNAs (lncRNAs): Identification and Functional Interpretation of lncRNAs from RNA-Seq Data Sets (Hai-Xi Sun, Nam-Hai Chua)....Pages 197-205
Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants (Song Qi, Shamima Akter, Song Li)....Pages 207-221
An Easy-to-Follow Pipeline for Long Noncoding RNA Identification: A Case Study in Diploid Strawberry Fragaria vesca (Chunying Kang, Zhongchi Liu)....Pages 223-243
Reference-Based Identification of Long Noncoding RNAs in Plants with Strand-Specific RNA-Sequencing Data (Xiao Lin, Meng Ni, Zhixia Xiao, Ting-Fung Chan, Hon-Ming Lam)....Pages 245-255
NAMS: Noncoding Assessment of long RNAs in Magnoliophyta Species (Gaurav Sablok, Kun Sun, Hao Sun)....Pages 257-264
De Novo Plant Transcriptome Assembly and Annotation Using Illumina RNA-Seq Reads (Stephanie C. Kerr, Federico Gaiti, Milos Tanurdzic)....Pages 265-275
Front Matter ....Pages 277-277
Identification of Long Noncoding RNA-Protein Interactions Through In Vitro RNA Pull-Down Assay with Plant Nuclear Extracts (Jun Sung Seo, Nam-Hai Chua)....Pages 279-288
Analysis of Interaction Between Long Noncoding RNAs and Protein by RNA Immunoprecipitation in Arabidopsis (Jun Sung Seo, Nam-Hai Chua)....Pages 289-295
Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants (Jun Sung Seo, Nam-Hai Chua)....Pages 297-303
In Vivo Genome-Wide RNA Structure Probing with Structure-seq (Laura E. Ritchey, Zhao Su, Sarah M. Assmann, Philip C. Bevilacqua)....Pages 305-341
Using Protein Interaction Profile Sequencing (PIP-seq) to Identify RNA Secondary Structure and RNA–Protein Interaction Sites of Long Noncoding RNAs in Plants (Marianne C. Kramer, Brian D. Gregory)....Pages 343-361
Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants (Mengge Shan, Zachary D. Anderson, Brian D. Gregory)....Pages 363-380
Stalking Structure in Plant Long Noncoding RNAs (Karissa Y. Sanbonmatsu)....Pages 381-388
Transcriptome-Wide Mapping 5-Methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant (Xiaofeng Gu, Zhe Liang)....Pages 389-394
Front Matter ....Pages 395-395
A Walkthrough to the Use of GreeNC: The Plant lncRNA Database (Andreu Paytuvi-Gallart, Walter Sanseverino, Riccardo Aiese Cigliano)....Pages 397-414
CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs (Michał Wojciech Szcześniak, Oleksii Bryzghalov, Joanna Ciomborowska-Basheer, Izabela Makałowska)....Pages 415-429
Experimentally Validated Plant lncRNAs in EVLncRNAs Database (Bailing Zhou, Huiying Zhao, Jiafeng Yu, Chengang Guo, Xianghua Dou, Feng Song et al.)....Pages 431-437
Front Matter ....Pages 439-439
In Situ Hi-C for Plants: An Improved Method to Detect Long-Range Chromatin Interactions (Sudharsan Padmarasu, Axel Himmelbach, Martin Mascher, Nils Stein)....Pages 441-472
Back Matter ....Pages 473-480

✦ Subjects

Life Sciences; Plant Sciences; Plant Genetics and Genomics