Plant MicroRNAs Methods and Protocols

About this book

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 this volume, 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.

Contents

1. Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana Zhixin Xie 2. Prediction of Plant miRNA Genes Matthew W. Jones-Rhoades 3. Methods for Isolation of Total RNA to Recover miRNAs and Other Small RNAs from Diverse Species Monica Accerbi, Skye A. Schmidt, Emanuele De Paoli, Sunhee Park, Dong-Hoon Jeong, and Pamela J. Green 4. miRNA Target Prediction in Plants Noah Fahlgren and James C. Carrington 5. A Method to Discover Phased siRNA Loci Michael J. Axtell 6. Directed Gene Silencing with Artificial MicroRNAs Rebecca Schwab, Stephan Ossowski, Norman Warthmann, and Detlef Weigel 7. Bioinformatics Analysis of Small RNAs in Plants Using Next Generation Sequencing Technologies Kan Nobuta, Kevin McCormick, Mayumi Nakano, and Blake C. Meyers 8. High-Throughput Approaches for miRNA Expression Analysis Cheng Lu and Fred Souret 9. In situ Detection of miRNAs Using LNA Probes Zoltan Havelda 10. Analysis of miRNA Modifications Bin Yu and Xuemei Chen 11. MicroRNA Promoter Analysis Molly Megraw and Artemis G. Hatzigeorgiou 12. Computational Methods for Comparative Analysis of Plant Small RNAs Gayathri Mahalingam and Blake C. Meyers 13. Biotic Stress-Associated microRNAs: Identification, Detection, Regulation, and Functional Analysis Florence Jay and Lionel Navarro 14. Abiotic Stress-Associated miRNAs: Detection and Functional Analysis Dong-Hoon Jeong, Marcelo A. German, Linda A. Rymarquis, Shawn R. Thatcher, and Pamela J. Green 15. Processing of miRNA Precursors Yukio Kurihara and Yuichiro Watanabe 16. Purification of Arabidopsis Argonaute Complexes and Associated Small RNAs Yijun Qi and Shijun Mi 17. Transient Assays for the Analysis of miRNA Processing and Function Felipe F. de Felippes and Detlef Weigel

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