RNA-Chromatin Interactions: Methods and Protocols

This second edition volume expands on the previous edition with an update on the latest methods used to study next-generation sequencing for large-scale analysis of nascent RNA and chromatin features associated with RNA function, as well as advanced techniques for functional studies of non-coding RNA function in the nucleus. The chapters in this book cover topics such as using BruUV-seq and TT-seq to identify enhancer RNA expression in live cells; revealing high-resolution open chromatin-associated interactions by NicE-C; purification of RNA G-quadruplex binding proteins; examining RNA modifications on chromatin or formation of R-loops; measuring the proximity of nuclear lncRNAs to nuclear bodies; and Cas13d-mediated knockdown of long non-coding RNAs. 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. Timely and comprehensive, RNA-Chromatin Interactions: Methods and Protocols, Second Edition is a valuable resource for new and experienced researchers in the RNA-chromatin field who want to expand their work to uncover new and exciting molecular mechanisms in both basic research and more disease-focused work.