Plant MicroRNAs Methods and Protocols

This second volume is a collection of new and updated protocols to study miRNA functions in plants.  Chapters guide readers from the identification and detection of plant miRNAs, bioinformatic analyses, to strategies for functional analysis of miRNAs and their targets. Furthermore, it contains a few introductory chapters on plant miRNA functioning and, on their conservation, and evolution. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Plant MicroRNAs: Methods and Protocols, Second Edition aims to provide protocols to help new researchers while also supporting established researchers to broaden the scope of their investigations.

The Use of Arabidopsis thaliana to Characterize the Production and Action Stages of the Plant MicroRNA Pathway.- An overview of miRNA and miRNA target analysis tools.- Prediction of miRNA targets in plants.- An overview of miRNA and miRNA target analysis tools.- Scalable Approach to Evaluate Plant microRNA Trimming and Tailing from Small RNA-Seq data.- In vitro transcription of plant miRNA for structural and processing analysis.- Cost-Effective and Sensitive Probe-Based Universal (PBU) qPCR for MicroRNA Quantification in Plants.- Northern blot analysis of plant microRNAs and other small RNAs.- Northern blot analysis of plant microRNAs and other small RNAs.- Determination of expression patterns of plant miRNAs by Transcriptional Fusion     using GUS and Fluorescent reporters.- A Visual Reporter System for Analyzing Small RNA-Triggered Local and Systemic Silencing of an Endogenous Plant Gene.- Unravelling tissue specific miRNAs role in plants exploiting the GAL4/UAS system. -The Luciferase reporter on intronic microRNA-directed regulation.- A simple and efficient protocol to transform and regenerate CRISPR-Cas9-mediated genome edited tomato plants.- CRISPR-activation: boosting expression of plant MIRs.- Gene silencing in plants through exogenous application of miRNAs.- A strategy to use Artificial MicroRNAs for Gene silencing and Overcome (AmiGO).- Degradome sequencing.- Whole mount staining and immunolocalization procedures for developing ovules of Vigna unguiculata.- Bioinformatic enrichment and network analyses of miRNA-related high-throughput sequencing data.- Identifying cis-regulatory binding sites in promoter regions of miRNA genes: A step-by-step protocol.- A Detailed Protocol for the Isolation of Arabidopsis thaliana Mesophyll Protoplasts and their Applications.- A protocol for live imaging of Arabidopsis gynoecium development using confocal microscopy.