Structural imprints in vivo decode RNA regulatory mechanisms

The single-stranded nature of RNAs synthesized in the cell gives them great scope to form different structures, but current methods to measure RNA structure in vivo are limited; now, a new methodology allows researchers to examine all four nucleotides in mouse embryonic stem cells. Probing native RNA structure The single-stranded nature of cellular RNAs allows them flexibility to adopt different secondary structures that can affect their function. However, current methods of measuring RNA structure in vivo are limited. Two papers published in this week's issue of Nature present new techniques to address this gap. Howard Chang and colleagues have exploited a click methodology that enables the first global view of RNA secondary structures in living cells for all four bases. While some structures are stable and seem to be programmed by sequence, others are dynamic, reflecting the binding of proteins or modification of the bases. This method may allow RNA to be analysed in vivo from a structural genomics perspective. In the second study, Jernej Ule and colleagues have developed a method, hiCLIP, to specifically measure RNA structures bound by proteins. Various features are observed, such as a preference for intramolecular interactions and an under-representation of structures in coding regions. The results confirm that RNA structure is able to regulate gene expression. While the functional significance is not known, it is notable that SNPs are not present at the expected frequency in coding regions. Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program 1 . However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA 2 , 3 . Here we present a novel biochemical approach, in vivo click selective 2′-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosom