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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.

Plant Long Non-Coding RNAs

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 Transcriptome 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.- Transcriptome-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.