Fig. 4

In vivo SHALiPE-Seq reveals hundreds of folded RG4s in rice. a Schematic of in vivo SHALiPE-Seq in rice. The in vivo folding state of the G-rich region is evaluated by comparing SHALiPE profiles in vivo with SHALiPE profiles in vitro in the presence of Li⁺ or K⁺, respectively. b Cumulative plot of Gini index of rice G-rich regions in vivo, in vitro with Li⁺ and in vitro with K⁺. A significantly higher Gini in vivo than in vitro with Li⁺ indicates the folding state of G-rich regions in vivo. P value, paired Student’s t test. c Histogram of in vivo folding score (FS) in rice. The median value is 0.938. The FS of 0 represents the unfolded states (with Li⁺) and 1 represents the folded states of RG4s (with K⁺) in vitro. d, e SHALiPE profiles of the RG4 region on LOC_Os02g15810 (d) and LOC_Os07g41694 (e). The in vivo SHALiPE profile resembled the in vitro SHALiPE profile with K⁺ (the last Gs of G-tracts indicated by black arrows) but not the in vitro SHALiPE profile with Li⁺, indicating the folded state of this RG4 in vivo. f Violin plot of in vivo folding scores of G-rich regions of different types. Folding scores of RG4s of different catalogues are similar (P values > 0.05, one-way ANOVA/Tukey HSD post hoc test). g Violin plot of in vivo folding scores of G-rich regions in CDS and UTRs. Folding scores of RG4s of different genic regions are similar (P > 0.05, one-way ANOVA/Tukey HSD post hoc test)