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Preface… Table of Contents… Contributing Authors… 1. Cloning and Identification of Recombinant-Argonaute Bound Small RNAs using Next-Generation Sequencing Pooja Gangras, Daniel M. Dayeh, Justin M. Mabin, Kotaro Nakanishi, and Guramrit Singh 2. Quantification of miRNAs Co-Immunoprecipitated with Argonaute Proteins using SYBR Green-Based qRT-PCR Hong-Duc Phan, Junan Li, Ming Poi, and Kotaro Nakanishi 3. Gateway to Understanding Argonaute Loading of Single-Stranded RNAs: Preparation of Deep Sequencing Libraries with In Vitro Loading Samples Eling Goh and Katsutomo Okamura 4. Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant Megumi Shigematsu, Shozo Honda, and Yohei Kirino 5. MicroRNA Detection by Whole-Mount In Situ Hybridization in C. elegans Yoshiki Andachi and Yuji Kohara 6. cCLIP-Seq: Retrieval of Chimaeric Reads from HITS-CLIP (CLIP-Seq) Libraries Panagiotis Alexiou, Manolis Maragkakis, Zissimos Mourelatos, and Anastassios Vourekas 7. Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro Susan E. Liao and Ryuya Fukunaga 8. Nucleic Acid-Binding Assay of Argonaute Protein using Fluorescence Polarization Tomohiro Miyoshi 9. Reconstitution of RNA Interference Machinery Shintaro Iwasaki and Yukihide Tomari 10. Single-Molecule Analysis for RISC Assembly and Target Cleavage Hiroshi M. Sasaki, Hisashi Tadakuma, and Yukihide Tomari 11. Profiling Open Chromatin Structure in the Ovarian Somatic Cells using ATAC-Seq Kensaku Murano, Yuka W. Iwasaki, and Haruhiko Siomi 12. Assessing miR-451 Activity and Its Role in Erythropoiesis Dmitry A. Kretov, Andrew M. Shafik, and Daniel Cifuentes 13. Functional Analysis of MicroRNAs in Neurogenesis during Mouse Cortical Development Wei Zhang, Xiaoxia Zeng, and Li Zeng 14. Cellular Approaches in Investigating Argonaute2-Dependent RNA Silencing Cai Zhang, Joonbae Seo, and Takahisa Nakamura 15. Genomic Tagging of AG01 using CRISPR/Cas9-Mediated Homologous Recombination Sanjay Ghosh and Ji-Long Liu 16. Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A vade mecum for MINTmap Phillipe Loher, Aristeidis G. Telonis, and Isidore Rigoutsos