Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana -- Prediction of Plant miRNA Genes -- Methods for Isolation of Total RNA to Recover miRNAs and Other Small RNAs from Diverse Species -- miRNA Target Prediction in Plants -- A Method to Discover Phased siRNA Loci -- Directed Gene Silencing with Artificial MicroRNAs -- Bioinformatics Analysis of Small RNAs in Plants Using Next Generation Sequencing Technologies -- High-Throughput Approaches for miRNA Expression Analysis -- In Situ Detection of miRNAs Using LNA Probes -- Analysis of miRNA Modifications -- MicroRNA Promoter Analysis -- Computational Methods for Comparative Analysis of Plant Small RNAs -- Biotic Stress-Associated microRNAs: Identification, Detection, Regulation, and Functional Analysis -- Abiotic Stress-Associated miRNAs: Detection and Functional Analysis -- Processing of miRNA Precursors -- Purification of Arabidopsis Argonaute Complexes and Associated Small RNAs -- Transient Assays for the Analysis of miRNA Processing and Function.

MicroRNAs constitute a particularly important class of small RNAs given their abundance, broad phylogenetic conservation and strong regulatory effects, with plant miRNAs uniquely divulging their ancient evolutionary origins and their strong post-transcriptional regulatory effects. In Plant MicroRNAs: Methods and Protocols, experts in the field present chapters that focus on the identification, validation, and characterization of the miRNA class of RNAs, and address important aspects about heterochromatic small interfering RNAs. In addition, the methods contained in this volume emphasize miRNA analyses, but also include ways to distinguish one class of small RNAs from another. As a volume in the highly successful Methods in Molecular Biology™ series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easy to use, Plant MicroRNAs: Methods and Protocols provides the research community with a set of protocols that will help advance vital miRNA research for all plant species, both in typical model species and non-model species alike.