Pirna: Methods and Protocols

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

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

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 Ca