Techniques for Analyzing Genome-wide Expression of Non-coding RNA

The development of RNA sequencing (RNA-seq) has revealed that most genomic regions are transcribed pervasively, resulting in the production of a large number of non-coding RNAs (ncRNAs), such as large intergenic ncRNAs, microRNAs, and enhancer RNAs. Many ncRNAs have now been shown to be involved in epigenetic gene regulation. The diversity of ncRNAs raises a major challenge to understand their structures, transcriptional regulation, processing, localization, and degradation. Here we introduce several key steps in RNA-seq that enable detection of ncRNAs, such as sample preparation optimized for ncRNAs, and computational annotation of ncRNAs from RNA-seq data. We also review the methods used for functional studies of ncRNAs, focusing on applications based on RNA-seq.