This volume explores the latest techniques and protocols used by researchers to address unique biological questions, model organisms not typically studied by Fluorescent In Situ Hybridization (FISH), protocols combining FISH with immunofluorescence (FISH-IF), and high-throughput experiments. The chapters in this book are divided into two parts: RNA FISH protocols and DNA FISH protocols. Part One covers methods for designing OligoPaint probes and studying distinct aspects of RNA biology such as transcription and splicing dynamics, and mRNA and small RNA expression and localization. Part Two discusses DNA repair dynamics, gene compaction, and chromatin conformation and gene rearrangements in plants, insects, and mammalian cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting edge and thorough, Fluorescence In Situ Hybridization (FISH): Methods and Protocols is a valuable resource that will benefit the broader scientific community in their studies and understanding of this important field.