RNA Silencing

1. Front Matter

   Pages i-xi

   PDF

2. Identification of Components of RNAi Pathways Using the Tandem Affinity Purification Method

   • Mikiko C. Siomi, Haruhiko Siomi

   Pages 1-9

3. Separation of Drosophila RNA Silencing Complexes by Native Gel Electrophoresis

   • John W. Pham, Erik J. Sontheimer

   Pages 11-16

4. Preparation and Analysis of Drosha

   • Yoontae Lee, V. Narry Kim

   Pages 17-28

5. RNA Interference in Caenorhabditis elegans

   • Nathaniel R. Dudley, Bob Goldstein

   Pages 29-38

6. Down-Regulating Gene Expression by RNA Interference in Trypanosoma brucei

   • Christine E. Clayton, Antonio M. Estévez, Claudia Hartmann, Vincent P. Alibu, Mark Field, David Horn

   Pages 39-59

7. Analysis of Double-Stranded RNA and Small RNAs Involved in RNA-Mediated Transcriptional Gene Silencing

   • M. Florian Mette, Werner Aufsatz, Tatsuo Kanno, Lucia Daxinger, Philipp Rovina, Marjori Matzke et al.

   Pages 61-82

8. Strategies for the Design of Random siRNA Libraries and the Selection of anti-GFP siRNAs

   • Mouldy Sioud, Sébastien Wälchli

   Pages 83-91

9. Silencing Gene Expression with Dicer-Generated siRNA Pools

   • Jason W. Myers, James E. Ferrell Jr.

   Pages 93-196

10. Inhibition of Gene Expression In Vivo Using Multiplex siRNA

    • Sung-Suk Chae, Timothy Hla

    Pages 197-203

11. Gene Silencing by a DNA Vector-Based RNAi Technology

    • Guangchao Sui, Yang Shi

    Pages 205-218

12. Plasmid-Based RNA Interference

    • Scott Q. Harper, Beverly L. Davidson

    Pages 219-235

13. siRNA Delivery In Vivo

    • Mouldy Sioud

    Pages 237-249

14. Peptide-Based Strategy for siRNA Delivery into Mammalian Cells

    • Federica Simeoni, May C. Morris, Frederic Heitz, Gilles Divita

    Pages 251-260

15. Lentiviral Vector Delivery of siRNA and shRNA Encoding Genes into Cultured and Primary Hematopoietic Cells

    • Mingjie Li, John J. Rossi

    Pages 261-272

16. Exon-Specific RNA Interference

    • Alicia M. Celotto, Joo-Won Lee, Brenton R. Graveley

    Pages 273-282

17. Immunoprecipitation of MicroRNPs and Directional Cloning of MicroRNAs

    • Elisavet Maniataki, Maria Dels Angels De Planell Saguer, Zissimos Mourelatos

    Pages 283-294

18. Detection of MicroRNAs and Assays to Monitor MicroRNA Activities In Vivo and In Vitro

    • Marianthi Kiriakidou, Peter Nelson, Stella Lamprinaki, Anup Sharma, Zissimos Mourelatos

    Pages 295-310

19. High-Throughput Analysis of MicroRNA Gene Expression Using Sensitive Probes

    • Mouldy Sioud, Øystein Røsok

    Pages 311-320

20. Modification of Human U1 snRNA for Inhibition of Gene Expression at the Level of Pre-mRNA

    • Peng Liu, Mary Louise Stover, Alexander Lichtler, David W. Rowe

    Pages 321-331

A collection of readily reproducible methods for the design, preparation, and use of RNAs for silencing gene expression in cells and organisms. The techniques range widely and include methods addressing the biochemical aspects of the silencing machinery, RNA silencing in non-mammalian organisms, and the in vivo delivery of siRNAs and silencing vectors. There are also techniques for designing, preparing, and using RNAs to silence gene expression, for fine-tuning regulation by targeting specific isoforms of a given gene, and for the study and use of microRNAs. The protocols follow the successful Methods in Molecular Biology™ series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

• DNA
• Vivo
• gene expression
• genes
• molecular biology
• regulation
• transcription

From the reviews:

"RNA Silencing: Methods and Protocols is a comprehensive and user-friendly reference and worth recommending. Researchers who are interested in using siRNA as a major method to do gene knockdown experiments in vitro to study gene function instead of using time-consuming gene targeting in mice and those who are interested in studying the functions of genes in the development of cell defense against viruses will find this book an excellent resource." (Weimin He, In Vitro Cellular & Developmental Biology - Animal, Vol. 42, May and June, 2006)

• Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington

  Gordon G. Carmichael

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