Advances in RNA structure analysis by chemical probing

Abstract

RNA is arguably the most versatile biological macromolecule due to its ability both to encode and to manipulate genetic information. The diverse roles of RNA depend on its ability to fold back on itself to form biologically functional structures that bind small molecules and large protein ligands, to change conformation, and to affect the cellular regulatory state. These features of RNA biology can be structurally interrogated using chemical mapping experiments. The usefulness and applications of RNA chemical probing technologies have expanded dramatically over the past five years due to several critical advances. These innovations include new sequence-independent RNA chemistries, algorithmic tools for high-throughput analysis of complex data sets composed of thousands of measurements, new approaches for interpreting chemical probing data for both secondary and tertiary structure prediction, facile methods for following time-dependent processes, and the willingness of individual research groups to tackle increasingly bold problems in RNA structural biology.

Long Noncoding RNAs: Past, Present, and Future

“…(C) Structural features: ncRNAs form specific secondary (base pairing) and tertiary (three-dimensional) structures to carry out their functions. Such structures can be mapped using chemical reagents that cleave at specific nucleotides or attack solvent-exposed regions of the RNA backbone or by cross-linking three-dimensionally proximal regions of the RNA to reveal long-range intramolecular interactions (Weeks 2010). Ribonucleases with different cleavage specificities are also used to identify single-or double-stranded regions, as well as protein-protected regions (RNase footprinting).…”

New insights into RNA secondary structure in the alternative splicing of pre-mRNAs

“…29 Nevertheless, more research is needed to verify these structures and to determine how ligands. 25 For both chemical and enzymatic probing, RNA accessibility is the major criterion for reactivity. Chemical probing yields information at the atomic level, whereas enzymatic probing yields information on helical and non-helical regions.…”

Determination of in vivo RNA structure in low-abundance transcripts

“…Knowledge of RNA structure in vivo therefore provides important insights regarding the evolution and function of biological systems. For decades, chemical and enzymatic probing have been among the most common and powerful assays available to obtain structural information on RNA at nucleotide resolution [2][3][4][5] . This information can dramatically improve secondary structure prediction [6][7][8] .…”