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Fig. 2 | Genome Biology

Fig. 2

From: RNA G-quadruplex structures exist and function in vivo in plants

Fig. 2

SHALiPE-Seq determines folding states of G-rich regions robustly. a Schematic of SHALiPE-Seq in vitro with K+ and Li+. In vitro probing in the presence of K+ and Li+ established the benchmarks of folded and unfolded states of G-rich regions, respectively. NAI (indicated by red cross) preferentially modifies the last G in G tracts of folded RG4s, resulting in a high Gini index of read counts (reads on preferentially modified Gs were in red) in SHALiPE profiles. In contrast, the distribution of the SHALiPE profile for the unfolded state in the presence of Li+ is uniform, resulting in a low Gini. b For G-rich regions detected using rG4-seq in the presence of K+, Gini of SHALiPE profiles in vitro with K+ (folded state) was greater than that of in vitro with Li+ (unfolded state) by a factor of 1.20 (n = 117, P value, paired Student’s t test, average read coverage on G ≥ 50 reads/nt). c, d rG4-seq profiles of G2 G-rich region on AT5G05380 (c) and G3 G-rich region on AT5G62670 (d). The 3′end of the G-rich region is indicated by a red triangle. A (blue), C (light grey), G (yellow) and U (green). e, f SHALiPE profiles in vitro with K+ or Li+ of G2 G-rich region on AT5G05380 (e) and G3 G-rich region on AT5G62670 (f). High read counts of last guanines of G-tracts (indicated by black arrows) represent strong modifications of NAI on these guanines in the presence of K+, indicating RG4s are folded. In the presence of Li+, last Gs are not strongly modified, representing the unfolded state of these G-rich regions. The Gini values with K+ are higher than those with Li+, as indicated. A (blue), C (light grey), G (yellow) and U (green)

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