Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
For some Rfam families, Transat highlights regions which are devoid of transient structures, thereby indicating regions of the RNA sequence which may be bound by other molecules early on in the folding process.
Shown here are two examples, the CsrB/RsmB RNA family (left, RF00018) and the bacterial tmRNA (right, RF00023) for a p-value threshold value of (left and right, top) and (right, bottom). The CsrB/RsmB RNA is known to be bound by multiple copies of the CsrA protein. The RNA's known structure comprises only short range helices and Transat predicts only two transient structures for the entire 392 bp long alignment. Both findings support the hypothesis that protein binding occurs early during the folding of this RNA. The helices of the pseudo-knotted known structure for the bacterial tmRNA are correctly predicted by Transat for a p-value threshold of (right, top). Transat predicts several additional helices, but the region of the tmRNA sequences that contains the reading frame which ends in a translation stop signal is devoid of statistically significant transient helices (right, bottom) supporting the hypothesis that the sequence in that region of the has been chosen to remain single-stranded and readily accessible. See the text or the caption of Figure 9 for more information on arc-plots.