Argonaute Proteins: Methods and Protocols

✍ Scribed by Katsutomo Okamura, Kotaro Nakanishi (eds.)

• Publisher: Humana Press
• Year: 2018
• Tongue: English
• Leaves: 262
• Series: Methods in Molecular Biology 1680
• Edition: 1
• Category: Library

✦ Synopsis

This volume covers methods that analyze various Argonaute proteins from a variety of organisms to help researchers better understand their properties ranging from a molecular level to an organismal level. The chapters in this book explore the following topics: identification and expression analysis of guide nucleic acids and their targets; analysis of biochemical properties of Argonautes; biological functions of Argonautes; and obtaining materials and setting up analysis platforms. 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.

Cutting-edge and authoritative, Argonaute Proteins: Methods and Protocols is a valuable resource for researchers and scientists looking to expand their knowledge of Argonaute proteins and their functions.

✦ Table of Contents

Front Matter ....Pages i-xiii
Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing (Pooja Gangras, Daniel M. Dayeh, Justin W. Mabin, Kotaro Nakanishi, Guramrit Singh)....Pages 1-28
Quantification of miRNAs Co-Immunoprecipitated with Argonaute Proteins Using SYBR Green-Based qRT-PCR (Hong-Duc Phan, Junan Li, Ming Poi, Kotaro Nakanishi)....Pages 29-40
Gateway to Understanding Argonaute Loading of Single-Stranded RNAs: Preparation of Deep Sequencing Libraries with In Vitro Loading Samples (Eling Goh, Katsutomo Okamura)....Pages 41-63
Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant (Megumi Shigematsu, Shozo Honda, Yohei Kirino)....Pages 65-73
MicroRNA Detection by Whole-Mount In Situ Hybridization in C. elegans (Yoshiki Andachi, Yuji Kohara)....Pages 75-86
cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries (Panagiotis Alexiou, Manolis Maragkakis, Zissimos Mourelatos, Anastassios Vourekas)....Pages 87-100
Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro (Susan E. Liao, Ryuya Fukunaga)....Pages 101-121
Nucleic Acid-Binding Assay of Argonaute Protein Using Fluorescence Polarization (Tomohiro Miyoshi)....Pages 123-129
Reconstitution of RNA Interference Machinery (Shintaro Iwasaki, Yukihide Tomari)....Pages 131-143
Single-Molecule Analysis for RISC Assembly and Target Cleavage (Hiroshi M. Sasaki, Hisashi Tadakuma, Yukihide Tomari)....Pages 145-164
Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq (Kensaku Murano, Yuka W. Iwasaki, Haruhiko Siomi)....Pages 165-177
Assessing miR-451 Activity and Its Role in Erythropoiesis (Dmitry A. Kretov, Andrew M. Shafik, Daniel Cifuentes)....Pages 179-190
Functional Analysis of MicroRNAs in Neurogenesis During Mouse Cortical Development (Wei Zhang, Xiaoxia Zeng, Li Zeng)....Pages 191-203
Cellular Approaches in Investigating Argonaute2-Dependent RNA Silencing (Cai Zhang, Joonbae Seo, Takahisa Nakamura)....Pages 205-215
Genomic Tagging of AGO1 Using CRISPR/Cas9-Mediated Homologous Recombination (Sanjay Ghosh, Ji-Long Liu)....Pages 217-235
Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap (Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos)....Pages 237-255
Back Matter ....Pages 257-260

✦ Subjects

Protein Science