Measuring RNA structure transcriptome-wide with icSHAPE

RNA molecules can be found at the heart of nearly every aspect of gene regulation: from gene expression to protein translation. The ability of RNA molecules to fold into intricate structures guides their function. Chemical methods to measure RNA structure have been part of the RNA biologists toolkit for several decades. These methods, although often cumbersome and difficult to perform on large RNAs, are notable for their accuracy and precision of structural measurements. Recent extension of these methods to transcriptome-wide analyses has opened the door to interrogating the structure of complete RNA molecules inside cells. Within this manuscript we describe the biochemical basis for the methodology behind a novel technology, icSHAPE, which measures RNA flexibility and single-strandedness in RNA. Novel methods such as icSHAPE have greatly expanded our understanding of RNA function and have paved the way to expansive analyses of large groups of RNA structures as they function inside the native environment of the cell.