Description
Book SynopsisThis detailed volume explores newly-developed methods in PIWI-interacting RNAs (piRNAs) research, methods currently applied to other ncRNAs involved in nuclear regulation which can be used to study piRNAs, and piRNA methods applied in non-classical organisms. It also includes several bioinformatic and biophysical methods related to piRNA studies, consistent with the increasing importance of high-throughput sequencing and computational methods. Written for the highly successful
Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and up-to-date, piRNA: Methods and Protocols serves as an ideal guide for researchers seeking to elucidate the numerous mysteries of this area of multicellular biology.
Table of ContentsPart I: Methods to Study the Nature and Function of piRNAs in Non-Classical Organisms
1. Functional Analysis of Individual piRNAs in Aedes aegypti Cells and Embryos Using Antisense Oligonucleotides
Rebecca Halbach and Pascal Miesen
2. CRISPR-Mediated Genome Engineering in Aedes aegypti
Ruichen Sun, Ming Li, Conor J. McMeniman, and Omar S. Akbari
3. PIWI-Directed DNA Elimination for Tetrahymena Genetics
Salman Shehzada and Kazufumi Mochizuki
4. Planarian PIWI-piRNA Interaction Analysis Using Immunoprecipitation and piRNA-Sequencing
Makoto Kashima, Atsumi Miyata, and Norito Shibata
5. Isolation and Processing of Bovine Oocytes for Small RNA Sequencing
Minjie Tan, Helena T.A. van Tol, and Elke F. Roovers
6. 3D Imaging and In Situ Hybridization for Uncovering the Functions of MicroRNA in Rice Anther
Koji Koizumi and Reina Komiya
Part II: Methods to Study Roles of piRNAs in Classic Model Organisms
7. Cloning, Sequencing, and Linkage Analysis of piRNAs
Rippei Hayashi
8. Drosophila Genetic Resources for Elucidating piRNA Pathway
Kuniaki Saito
9. Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System
Chikara Takeuchi, Kensaku Murano, Mitsuru Ishikawa, Hideyuki Okano, and Yuka W. Iwasaki
Part III: Methods to Study Nuclear Regulation by Other Non-Coding RNAs
10. Whole Mount RNA FISH Combined with Immunofluorescence for Analysis of the Telomeric Ribonucleoproteins in the Drosophila Germline
Valeriya Morgunova, Maria M. Sukhova, and Alla Kalmykova
11. CRISPR-Mediated Activation of Transposable Elements in Embryonic Stem Cells
Akihiko Sakashita, Masaru Ariura, and Satoshi H. Namekawa
12. Method for Evaluating Effects of Non-Coding RNAs on Nucleosome Stability
Mariko Dacher, Risa Fujita, Tomoya Kujirai, and Hitoshi Kurumizaka
13. Revisiting the Glass Treatment for Single Molecule Analysis of ncRNA Function
Shuting Shen, Masahiro Naganuma, Yukihide Tomari, and Hisashi Tadakuma
14. Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification
Wan Kin Au Yeung and Hiroyuki Sasaki
15. Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq
Abd-El Monsif Shawky, Mahmoud Dondeti, Zissimos Mourelatos, and Anastasios Vourekas
16. UPA-Seq-Based Search Method for Functional lncRNA Candidates
Saori Yokoi and Shinichi Nakagawa
17. Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST
Emi Miyashita, Kaoru R. Komatsu, and Hirohide Saito
Part IV: Bioinformatic and Biophysical Methods to Study Non-Coding RNAs
18. Computational Methods for the Discovery and Annotation of Viral Integrations
Umberto Palatini, Elisa Pischedda, and Mariangela Bonizzoni
19. Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-Coding RNAs
Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, and Michiaki Hamada
20. Extending and Running the Mosquito Small RNA Genomics Resource Pipeline
Gargi Dayama, Katia Bulekova, and Nelson C. Lau
21. Preparation of Non-Overlapping Transposable Elements (TE) Annotation by Interval Tree
Shohei Kojima
22. Statistical Thermodynamics Approach for Intracellular Phase Separation
Tomohiro Yamazaki and Tetsuya Yamamoto
