piRNA

Methods and Protocols

Nicholas F. Parrish, Yuka W. Iwasaki (Herausgeber)

Buch | Softcover

397 Seiten

2023 | 1st ed. 2022
Springer-Verlag New York Inc.
978-1-0716-2382-4 (ISBN)

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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.

lt;p>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

Erscheinungsdatum	12.07.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	73 Illustrations, color; 10 Illustrations, black and white; XII, 397 p. 83 illus., 73 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Biochemie
	Naturwissenschaften ► Chemie
	Technik ► Maschinenbau
Schlagworte	Bioinformatics • Enzymatic pathways • Germline protection • Non-coding RNAs • piRNA biogenesis • PIWI-interacting RNAs
ISBN-10	1-0716-2382-6 / 1071623826
ISBN-13	978-1-0716-2382-4 / 9781071623824
Zustand	Neuware