For some RNAs, secondary, tertiary and quaternary structure relate to their functions. For example, the stem-loop structure found at the 3′-end of mammalian histone mRNAs confers stability to the transcript and plays a key role in the RNA 3′-end processing, and temporal regulation of histone expression (1-3).
Secondary and higher-order structure can influence protein binding to RNA and conversely, protein binding can influence RNA structure. For instance the TRAP complex reorganizes the secondary structure of the antiterminator of the trpEDCFBA operon in Bacillus subtilis to negate its function and down regulate transcription (4). The interplay of RNA structure and protein binding is an important theme throughout biology. In classic techniques RNA structure is studied by chemical or enzymatic mapping. These techniques capitalize on the differential sensitivity of structured regions to chemical modification, degradation, or nuclease digestion. In addition, the binding of proteins can alter the accessibility of RNA to modification and degradation allowing for binding events, and structural consequences to be interrogated. In vitro RNA structural studies often require in vitro transcribed RNA substrates and may require labeling for detection. Newer techniques such as SHAPE and PAR-CLIP, apply next generation sequencing to detect RNA that is modified in similar ways to more classic structural analysis approaches.