Next-generation sequencing technologies for detection of modified nucleotides in RNAs

Our ability to map and quantify RNA modifications at a genome-wide scale have revolutionized our understanding of the pervasiveness and dynamic regulation of diverse RNA modifications. Recent efforts in the field have demonstrated the presence of modified residues in almost any type of cellular RNA. Next-generation sequencing (NGS) technologies are the primary choice for transcriptome-wide RNA modification mapping. Here we provide an overview of approaches for RNA modification detection based on their RT-signature, specific chemicals, antibody-dependent (Ab) enrichment, or combinations thereof. We further discuss sources of artifacts in genome-wide modification maps, and experimental and computational considerations to overcome them. The future in this field is tightly linked to the development of new specific chemical reagents, highly specific Ab against RNA modifications and use of single-molecule RNA sequencing techniques.