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Architecture and secondary structure of an entire HIV-1 RNA genome

Joseph M. Watts, Kristen K. Dang, Robert J. Gorelick, Christopher W. Leonard, Julian W. Bess Jr, Ronald Swanstrom, Christina L. Burch & Kevin M. Weeks

Nature 460 (7256): 711-716, August 2009.
doi:10.1038/nature08237

This week’s snappy summary and analysis by Vikram Agarwal:

In this article, Watts and colleagues demonstrate a method to systematically predict the RNA secondary structure of an HIV-1 viral genome.  Their technique, called SHAPE (2′-hydroxyl acylation analysed by primer extension), exploits the principle that nucleotides in a flexible conformation can react with an electrophile that subsequently blocks a primer extension reaction.  In this way, one can visualize and quantify the tendency of regions of RNA to participate in base pairing or remain unstructured, all at single-nucleotide resolution.  The technique was recently shown to accurately predict nearly 95-100% of bases in rRNA, tRNA, and several coding RNAs (Deigan et al., PNAS 2009).  The SHAPE reactivity of each base position is converted linearly into a pseudo-free energy term, which is incorporated into RNAstructure to fold the entire RNA.

Here the foldings reconstruct known motifs in the HIV genome, such as the gag-pol frameshift element, which are shown here to actually be constituents of more extensive motifs.  Most notably, the technique allows the group to predict an accurate structure for all coding regions, which have been formidable to characterize using traditional approaches.  The paper finds significant correlations between RNA secondary structure and protein secondary structure, with inter-protein linkers and protein-domain junctions often corresponding to highly structured RNA regions.  This result implicates such highly structured regions in modulating and offering time for protein folding during translation.  To investigate this possibility, the authors perform a ribosomal toeprinting experiment on two HIV-1 open-reading frames to test the hypothesis that local RNA flexibility influences the pausing of a ribosome as it scans the RNA message (Supplementary Figure 5).

Overall, this paper contributes a notable advance in the accurate characterization of RNA structures on a large scale.  It opens the door for parallelization of SHAPE analysis to characterize even larger RNA genomes at high-resolution, which would open a wealth of knowledge about how RNA motifs and other signals are interpreted by the cell.  Moreover, it suggests a link between RNA structure and protein folding.  However, this link requires a more thorough and direct investigation in the future.  The authors establish only a correlative relationship between the RNA and protein structure, and have yet to dissect the underlying causality of the process.  This may ultimately merit mutational experiments that modify RNA secondary structure to examine if regions within a protein are differentially folded via the fine-tuning of ribosomal processivity by the base pairing interactions of RNA.