Description
Regulatory Non-Coding RNAs: Methods and Protocols offers a collection of methods for those interested in the discovery, localization, and functional analysis of these non-coding transcripts that have the potential and ability to orchestrate and control gene expression. After a review of the field, this detailed volume continues with methods useful for the study of siRNAs, microRNAs and their targets, techniques concerned with long non-coding RNAs, as well as studies of the critical parameters of functional non-coding RNA protein-RNA interactions and the environment in which they act. Written for 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 tips for troubleshooting and avoiding known pitfalls. Dependable and easy to use, Regulatory Non-Coding RNAs: Methods and Protocols provides a current, state-of-the-art collection of methods and approaches that will be of value to researchers in this expanding and fascinating field. 1. Diverse Functions and Mechanisms of Mammalian Long Non-Coding RNAs Callie R. Merry, Courtney Niland, and Ahmad M. Khalil 2. Sequence-Defined Oligoaminoamides for the Delivery of siRNAs Dian-Jang Lee, Ernst Wagner, and Taavi Lehto 3. A Biochemical Approach to Identify Direct MicroRNA Targets Murugan Subramanian, Xiao Ling Li, Toshifumi Hara, and Ashish Lal 4. Native Gel Analysis for Mammalian MicroRNPs Assembled from Pre-MicroRNAs Xuhang Liu and Zissimos Mourelatos 5. Identification and Validation of miRNA Target Sites within Non-Traditional miRNA Targets Scott T. Younger and David R. Corey 6. Fractionation of Non-Polyadenylated and Ribosomal-Free RNAs from Mammalian Cells Qing-Fei Yin, Ling-Ling Chen, and Li Yang 7. Affinity-Purification of Long Noncoding RNA-Protein Complexes from Formaldehyde-Crosslinked Mammalian Cells Chenguang Gong and Lynne Maquat 8. RNA Pulldown Protocol for In Vitro Detection and Identification of RNA-Associated Proteins Oskar Marn-Bjar and Maite Huarte 9. nRIP-seq: A Technique to Identify RNA Targets of an RNA Binding Protein on a Genome-Wide Scale Jing Crystal Zhao 10. Analysis of the Subcellular Distribution of RNA by Fluorescence In Situ Hybridization Shinichi Nakagawa 11. RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells Vidisha Tripathi, Jingyi Fei, Taekjip Ha, and Kannanganattu V. Prasanth 12. Locating RNAs In Situ with FISH-STIC Probes John R. Sinnamon and Kevin Czaplinski 13. Rapid and Efficient Elimination of Specific Nuclear Noncoding RNAs in Mammalian Cells with Antisense Oligonucleotides Tetsuro Hirose and Taro Mannen 14. On Using Magnesium and Potassium Ions in RNA Experiments Neena Grover 15. Studying the Affinity, Kinetic Stability, and Specificity of RNA/Protein Interactions: SINE ncRNA/Pol II Complexes as a Model System James A. Goodrich and Jennifer F. Kugel
