Cellular Fractionation and Isolation of Chromatin-associated RNA -- Knockdown of Nuclear-located Enhancer RNAs and Long ncRNAs using Locked Nucleic Acid GapmeRs -- Visualization of Enhancer-derived Non-coding RNA -- UV-RNA Immunoprecipitation (UV-RIP) Protocol in Neurons -- Mapping Long non-coding RNA Chromatin Occupancy using Capture Hybridization Analysis of RNA Targets (CHART) -- Detecting long-range Enhancer-promoter Interactions by Quantitative Chromosome Conformation Capture -- Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET) -- Identification of Transcribed Enhancers by Genome-wide Chromatin Immunoprecipitation Sequencing -- Global Run-On sequencing (GRO-seq) -- Computational Approaches for Mining GRO-seq Data to Identify and Characterize Active Enhancers -- Evaluating the Stability of mRNAs and Non-coding RNAs -- A Novel Method to Quantify RNA-protein Interactions in situ using FMTRIP and Proximity Ligation -- In silico Promoter Recognition from deepCAGE data -- Bioinformatics Pipeline for Transcriptome Sequencing Analysis -- CRISPR/Cas-9 Genome Editing in Embryonic Stem Cells -- Targeted Gene Activation Using RNA-Guided Nucleases.

This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long ncRNAs and exploring transcription by assessing where transcription starts and generally how it occurs.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. Authoritative and cutting-edge, Enhancer RNAs: Methods and Protocols aims to ensure successful results in this rapidly developing field.