Argonaute Proteins: Methods and Protocols

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