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…mehr
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.
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.
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.
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