Plant MicroRNAs: Methods and Protocols / Edition 1

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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 Prools, 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 prools, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easy to use, Plant MicroRNAs: Methods and Prools provides the research community with a set of prools that will help advance vital miRNA research for all plant species, both in typical model species and non-model species alike.

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Product Details

  • ISBN-13: 9781603270045
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 10/28/2009
  • Series: Methods in Molecular Biology Series, #592
  • Edition description: 2010
  • Edition number: 1
  • Pages: 261
  • Product dimensions: 10.00 (w) x 7.00 (h) x 0.69 (d)

Table of 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

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 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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