Chapter 11 – High-Throughput Analysis of Noncoding RNAs: Implications in Clinical Epigenetics

The evidence that protein-coding genes represent less than 2% of all human genome, and that more than 90% of it is actively transcribed, changed the shared view that RNA is a bridge between DNA sequences and proteins. The introduction of RNA-sequencing technology and the parallel expansion of computational biology revealed that thousands of sites produce noncoding transcripts. These molecules, collectively known as noncoding RNAs (ncRNAs), are key players in transcriptional and posttranscriptional regulation and in chromatin organization. Their altered expression is increasingly associated with pathological conditions. This chapter provides an overview about innovative high-throughput sequencing technologies and computational pipelines to profile ncRNAs, focusing on those with a proven epigenetic role. We also provide some guidelines to take into account when dealing with these molecules, from both the experimental and bioinformatics point of view. Furthermore, we examine the network between epigenome and ncRNAs, highlighting how these interactions are disrupted in human disease. Finally, we describe some pioneer studies that have demonstrated the potential use of ncRNAs as new diagnostic and/or prognostic biomarkers in the clinical practice.