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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.
List of contents
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 Treatmentfor 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.
