Fig. 3

The presence of G2 quadruplexes in the UTRs correlates with the expression of genes under heat stress. a, c Higher cumulative values of the normalized RPF reads to the mRNA reads at each position under heat stress-exposed plants (red) compared to the control plants (blue) over the positions of the putative G2 quadruplexes in the annotated 5′ UTRs (a) and 3′ UTRs (c). RPF coverage (rpm) was normalized to the mRNA reads at each position and each gene in the set is equally weighted. The first nucleotide of the G2 quadruplexes is at position 200. p-values (on the top of the plots) were calculated with the Wilcoxon signed rank test. b RPF fold change analysis of genes with G2 quadruplexes in their 5′ UTRs. Genes upregulated under thermal exposure (RPF up) were compared to genes with G2 quadruplexes but unchanged or downregulated under stress (RPF 0/down). Only reads in the CDSs were considered in this analysis. n denotes the gene number in each group. d RPF coverage profile of gene At3g56090 under heat stress exposure compared to its profile in the control plants. The position of the G2 quadruplex in the 5′UTR is shadowed in gray. In the gene scheme over the profiles: black, CDS; gray, 5′ or 3′ UTRs; gray dashed line, introns. e Comparison of the reads in the first vs. second halves of genes with G2 quadruplexes in their 3′ UTRs