Fig. 4

PARS reveals distinct RNA secondary structural signatures in functional units of transcripts. a. PARS scores across the 5’UTR, the coding region (CDS), and the 3’UTR of Zebrafish mRNAs are represented. PARS scores averaged across 451 transcripts with load > 1 and position coverage > 85%, aligned by the translational start and stop sites are represented. Averaged PARS scores and GC% are reported for regions are shaded in grey. b. Line graph representing average PARS scores and GC% across 25 nucleotides flanking the splice junctions of 451 transcripts are represented. c. Line graph displaying average PARS scores for last 50 nucleotides of the 3’ UTRs (n = 451) are represented. d. Line graph representing amplitude vs frequency of the Discrete Fourier Transform analysis of the average PARS scores of CDS, 3’ UTR and 5’ UTR corresponds to 451 transcripts. The highest frequency peak is obtained at 0.33 in CDS, showing a periodicity of 3 bases. e. Boxplot for average PARS scores for every codon position for first 100 CDS positions in 451 transcripts. The pairing probability of every position in a codon follows 1 > 2 > 3 (p value = 1.9e-07). Every position significantly differs from the other position by a p value = 1.702e-08 (ANOVA). f. Region-wise pattern of RNA secondary structures within enriched molecular function GO categories. The heatmap represents the region-wise (5’UTR, CDS and 3’UTR) significant p-values obtained from Wilcoxon rank sum test performed using the average PARS scores calculated for transcripts belonging to each enriched GO category. Red color suggests that genes belonging to the specific GO category shows under-structuring or lower PARS scores than the expected average PARS score for the region, where as shades of green depict over-structuring of genes belonging to the specific GO category in the respective regions. The asterisk * indicates that no significant conclusion can be drawn for a small number of genes (n = 2) in rRNA binding category