Pirna: Methods and Protocols

ISBN-13: 9781071623794 / Angielski / Twarda / 2022

Parrish, Nicholas F.

Opis

This 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.

Spis treści

Part 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