Functional Analysis of Individual piRNAs in Aedes aegypti Cells and Embryos Using Antisense Oligonucleotides -- CRISPR-Mediated Genome Engineering in Aedes aegypti -- PIWI-Directed DNA Elimination for Tetrahymena Genetics -- Planarian PIWI-piRNA Interaction Analysis Using Immunoprecipitation and piRNA-Sequencing -- Isolation and Processing of Bovine Oocytes for Small RNA Sequencing -- 3D Imaging and In Situ Hybridization for Uncovering the Functions of MicroRNA in Rice Anther -- Cloning, Sequencing, and Linkage Analysis of piRNAs -- Drosophila Genetic Resources for Elucidating piRNA Pathway -- Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System -- Whole Mount RNA FISH Combined with Immunofluorescence for Analysis of the Telomeric Ribonucleoproteins in the Drosophila Germline -- CRISPR-Mediated Activation of Transposable Elements in Embryonic Stem Cells -- Method for Evaluating Effects of Non-Coding RNAs on Nucleosome Stability -- Revisiting the Glass Treatment for Single Molecule Analysis of ncRNA Function -- Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification -- Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq -- UPA-Seq-Based Search Method for Functional lncRNA Candidates -- Large-Scale Analysis of RNA-Protein Interactions for Functional RNA Motif Discovery Using FOREST -- Computational Methods for the Discovery and Annotation of Viral Integrations -- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-Coding RNAs -- Extending and Running the Mosquito Small RNA Genomics Resource Pipeline -- Preparation of Non-Overlapping Transposable Elements (TE) Annotation by Interval Tree -- Statistical Thermodynamics Approach for Intracellular Phase Separation.

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.