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Plant Long Non-Coding RNAs

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Julia A. Chekanova

    1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China

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  2. Hsiao-Lin V. Wang

    1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
      Department of Biology, Emory University, Atlanta, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1933)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xvii
    Download chapter PDF

  2. 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

  3. Role of ncRNAs in Regulation of Gene Expression and Development in Plants

    1. Front Matter

      Pages 31-31
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    2. 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

    3. Identification of Long Noncoding RNAs in the Developing Endosperm of Maize

      • Eundeok Kim, Yuqing Xiong, Byung-Ho Kang, Sibum Sung
      Pages 49-65

    4. 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

  4. Studying the Tissue and Cell-Type Specific lncRNAs

    1. Front Matter

      Pages 87-87
      Download chapter PDF

    2. 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

    3. 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

    4. Purification and Functional Analysis of Plant Long Noncoding RNAs (lncRNA)

      • Trung Do, Zhipeng Qu, Iain Searle
      Pages 131-147

  5. Studying lncRNAs Associated with Response to Abiotic and Biotic Stresses in Plants

    1. Front Matter

      Pages 149-149
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    2. The Involvement of Long Noncoding RNAs in Response to Plant Stress

      • Akihiro Matsui, Motoaki Seki
      Pages 151-171

    3. Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance

      • Tao Qin, Liming Xiong
      Pages 173-186

    4. 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

  6. Identification and Functional Analysis of lncRNAs

    1. Front Matter

      Pages 195-195
      Download chapter PDF

    2. 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

    3. Identification of Novel lincRNA and Co-Expression Network Analysis Using RNA-Sequencing Data in Plants

      • Song Qi, Shamima Akter, Song Li
      Pages 207-221

    4. 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

    5. 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

    6. NAMS: Noncoding Assessment of long RNAs in Magnoliophyta Species

      • Gaurav Sablok, Kun Sun, Hao Sun
      Pages 257-264
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Keywords

About this book

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.

Editors and Affiliations

  • Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China

    Julia A. Chekanova, Hsiao-Lin V. Wang

  • Department of Biology, Emory University, Atlanta, USA

    Hsiao-Lin V. Wang

Bibliographic Information

  • Book Title: Plant Long Non-Coding RNAs

  • Book Subtitle: Methods and Protocols

  • Editors: Julia A. Chekanova, Hsiao-Lin V. Wang

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9045-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9044-3Published: 03 April 2019

  • eBook ISBN: 978-1-4939-9045-0Published: 03 April 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVII, 480

  • Number of Illustrations: 11 b/w illustrations, 67 illustrations in colour

  • Topics: Plant Sciences, Plant Genetics and Genomics

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