Fig 1.
SHAPE-based scoring function for structurally-informed RNA sequence alignment.
(A) Histogram of the absolute differences in SHAPE reactivities for paired nucleotides in accepted alignments. Differences between related pairs are shown in red, and differences between randomized pairs are blue. Pairs were randomized in eight individual trials; average values are shown with standard deviations given as error bars. (B) Scoring function used to compare SHAPE values at positions i and j in sequences x and y, respectively.
Fig 2.
Representative global sequence alignment between E. coli and C. difficile 16S ribosomal RNAs using model-free SHAPE reactivities as the only constraint.
Alignment is shown as a function of E. coli sequence numbering. (A) Alignment of SHAPE reactivities across a 250-nucleotide window. (B) A 60-nucleotide subsection of this alignment, including primary sequences. Areas of sequence identity are emphasized in bold.
Table 1.
Sensitivities of pairwise SHAPE-dependent sequence alignments relative to accepted alignments.
Table 2.
Sensitivities (sens) and positive predictive values (ppv) for secondary structure models as a function of included information.
Fig 3.
Secondary structure model for E. coli 16S rRNA.
This model was constrained by 16S rRNA consensus base pairs derived from SHAPE-based sequence alignment. Predicted pairs that exactly match the accepted covariation model [11] are shown with short black lines, and predicted pairs that match after modest local refolding are purple. Predicted pairs not in the covariation model are illustrated with blue lines. Covariation pairs not in the SHAPE-aligned structure are shown using red lines. E. coli SHAPE reactivities are shown by coloring of individual nucleotides (see scale). Areas with large-scale SHAPE-supported alternative folds are emphasized with cyan boxes. These areas (cyan) are illustrated on a structure model of the 16S ribosome [38] (bottom right) and cluster in the neck and decoding site. The inset is shown with an orientation that allows both h36 and the decoding site (h28 and h44) to be seen clearly.
Fig 4.
Consensus alternate structures for helix 36 of E. coli 16S rRNA.
(A) SHAPE reactivities for aligned regions with consensus areas (RNAalifold) highlighted in gray. (B) Structures for the covariation and SHAPE-structure constrained models. Base pairs predicted in the first-step (RNAalifold) consensus are black, and base pairs predicted in the follow-up constrained (RNAfold) prediction are shown in gray.
Fig 5.
Consensus alternate structures in the decoding site.
Helices 28 and 44 of the E. coli 16S rRNA are shown. (A) SHAPE reactivities for aligned regions. Consensus base pairs are highlighted in gray. (B) Structures for the covariation and SHAPE-structure constrained models. Base pairs in the RNAalifold consensus are shown in black, and base pairs predicted in the follow-up constrained RNAfold prediction are gray.