Fig. 2: PORE-cupine performs accurately in vitro and in vivo and captures riboswitch structural dynamics.
From: Determination of isoform-specific RNA structure with nanopore long reads
a–c, Graphs of z-score-normalized NAI-N3 modification profiles against SAFA footprinting signals from in vivo modified 16S rRNA (a), in vitro modified AdoCbl riboswitch (b) and in vitro modified RPS29 (c). The Pearson correlation was used to quantify the similarity between the two signals. SAFA quantification is shown as a bar chart in teal; PORE-cupine is shown as a line plot in black. d,e, PORE-cupine captures TPP riboswitch dynamics. d, Top, line plots showing PORE-cupine reactivities along TPP riboswitch in the presence of different concentrations of TPP (0, 250 nM, 750 nM and 10 μM). The pink box marks the aptamer region of the riboswitch, which shows the greatest change. Below, expanded view of the reactivities in the aptamer region. e, Pearson correlation between the reactivities of TPP when structure probed in water versus in the presence of 250 nM TPP, 750 nM TPP and 10 μM TPP. Pearson correlation values were computed by taking 30-nucleotide sliding windows across the transcript.
