Main description:

This detailed volume provides a collection of protocols for the study of miRNA functions in plants. Beginning with coverage of miRNA function, biogenesis, activity, and evolution in plants, the book continues by guiding readers through methods on the identification and detection of plant miRNAs, bioinformatic analyses, and strategies for functional analyses of miRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Plant MicroRNAs: Method and Protocols aims to ensure successful results in the further study of this vital area of plant science.

Contents:

1. An Introduction to Methods for Discovery and Functional Analysis of MicroRNAs in Plants

Alma Armenta-Medina and C. Stewart Gillmor

2. The Plant MicroRNA Pathway: The Production and Action Stages

Joseph L. Pegler, Christopher P. Grof, and Andrew L. Eamens

3. Plant miRNA Conservation and Evolution

Lydia Gramzow and Gunter Theissen

4. Bioinformatic Analysis of Small RNA Sequencing Libraries

Ricardo A. Chavez Montes, Fabiola Jaimes Miranda, and Stefan de Folter

5. An Overview of miRNA and miRNA Target Analysis Tools

Anna Lukasik and Piotr Zielenkiewicz

6. miRLocator: A Python Implementation and Web Server for Predicting miRNAs from Pre-miRNA Sequences

Ting Zhang, Lie Ju, Jingjing Zhai, Yujia Song, Jie Song, and Chuang Ma

7. Prediction of Plant miRNA Targets

Priyanka Pandey, Prashant K. Srivastava, and Shree P. Pandey

8. Isolation and Detection Methods of Plant miRNAs

Pedro Fernando Vera Hernandez, Stefan de Folter, and Flor de Fatima Rosas Cardenas

9. Northern Blot Analysis of MicroRNAs and Other Small RNAs in Plants

Carlos De la Rosa and Jose Luis Reyes

10. miRNA Detection by Stem-Loop RT-qPCR in Studying MicroRNA Biogenesis and MicroRNA Responsiveness to Abiotic Stresses

Aleksandra Smoczynska, Pawel Sega, Agata Stepien, Katarzyna Knop, Artur Jarmolowski, Andrzej Pacak, and Zofia Szweykowska-Kulinska

11. Detection of miRNAs by Tissue Printing and Dot Blot Hybridization

Marcelino Martinez Nunez, Stefan de Folter, and Flor de Fatima Rosas Cardenas

12. In Situ Localization of Small RNAs in Plants

Cristina F. Marco, Damianos S. Skopelitis, and Marja C.P. Timmermans

13. Expression Pattern of Plant miRNAs by Classical Transcriptional Fusion Constructs

Andrea Tovar-Aguilar, Karla A. Sanchez-Elizondo, Alejandra Rodriguez-Rodriguez, Marcos I. Gonzalez-Jaime, Genaro Patino-Lopez, Vadim Perez-Koldenkova, Jesus A. Badillo-Corona, and Noe Duran-Figueroa

14. A Simple Protocol for Imaging Floral Tissues of Arabidopsis with Confocal Microscopy

Andrea Gomez-Felipe and Stefan de Folter

15. Degradome Sequencing in Plants

Shih-Shun Lin, Yihua Chen, and Mei-Yeh Jade Lu

16. Functional Analysis of Root MicroRNAs by a Constitutive Overexpression Approach in a Composite Plant System

Damien Formey, Jose Angel Martin-Rodriguez, and Georgina Hernandez

17. The Use of MicroRNA Decoy Technologies to Inhibit miRNA Function in Arabidopsis

Gigi Wong and Anthony A. Millar

18. Mimicry Technology: A Versatile Tool for Small RNA Suppression

Luis Manuel Villar-Martin and Ignacio Rubio-Somoza

19. Design and High-Throughput Generation of Artificial Small RNA Constructs for Plants

Alberto Carbonell

20. Detection of MicroRNA Processing Intermediates through RNA Ligation Approaches

Belen Moro, Arantxa M.L Rojas, and Javier F. Palatnik

21. Analysis of Methylation Status of Plant MicroRNAs

Susu Chen and Guodong Ren

22. Detection of Slicer Activity by Immunopurified Plant ARGONAUTE1

Laura Arribas-Hernandez, Maria Louisa Vigh, and Peter Brodersen

23. The Isolation of Total and Membrane-Bound Polysomes from Arabidopsis and the Detection of Their Associated AGO1 and sRNAs

Shengben Li

24. Immunolocalization to Study ARGONAUTE Proteins in Developing Ovules of the Brassicaceae

Gloria Leon-Martinez, Edgar Demesa-Arevalo, and Jean-Philippe Vielle-Calzada

25. Detection of Histone Modifications Associated with miRNAs

Sara Hernandez-Castellano and Clelia De-la-Pena