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Plant MicroRNAs - Methods and Protocols

Edited by Meyers, Blake C.; Green, Pamela J. 
Springer  October 2009  



Hardcover  261 pp  ISBN 9781603270045      £72.00
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. This book presents 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.

Contents

Preface

Contributors

1 Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana, Zhixin Xie

2 Prediction of Plant miRNA GenesMatthew 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 MicroRNAsRebecca 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 Frédéric Souret

9 In Situ Detection of miRNAs Using LNA, Zoltán 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, Gayathri Mahalingam and Blake C. Meyers

13 Biotic Stress-Associated microRNAs: Identification, Detection, Regulation, and Functional Analysis, Florence Jay, Jean-Pierre Renou, Olivier Voinnet, 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

Index

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RNA : Springer : biochemistry : methods : molecular biology : plant science : protocols

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