Fig. 2: Cold promotes RNA G-quadruplex folding in Arabidopsis.
From: RNA G-quadruplex structure contributes to cold adaptation in plants
a Immunofluorescence detection of G-quadruplex (RG4) with BG4 antibody in Arabidopsis under different thermal conditions. Arabidopsis seedlings were grown at 22 °C (Control) and were (i) treated at 4 °C for 2 h (Cold); or (ii) returned to 22 °C for 2 h after cold treatment (Recovery); or (iii) treated with 10 μM pyridostatin (PDS); or (iv) treated with RNase cocktail (RNase). DAPI indicates the nucleus signal. Statistical analysis was performed using >80 cells from three individual seedlings for each treatment, with significance tested by Student’s t test in comparison to Control. b Comparison of RG4 folding by SHALiPE-seq in plants grown at 22 °C and treated either at 4 °C or 22 °C, respectively, n = 817, P < 10−148, by one-sided Student’s t test. SHALiPE-seq data were generated from two independent biological replicates. c SHALiPE-seq profiles of the RG4s on AT3G20470 (GRP5). High reads on the last Gs (dark arrow) are compared between in vitro benchmarks: either with K+ (RG4 folded) or Li+ (RG4 unfolded). In vivo profiles show an unfolded state at 22 °C (resembles the benchmark with Li+) but folded state at 4 °C (resembles that with K+). d Frequency of distinct RG4 motifs comparing folding score differences (4–22 °C) between G2-RG4 and G3-RG4 motifs; n = 1436, 51 for G2 and G3 sites, respectively, ***P = 0.006 by one-sided Student’s t test. e Comparison of RG4 folding score difference frequencies (4–22 °C) with different RG4 loop lengths. RG4 sites n = 104, 304, 243, 442, and 343 for loop length of 2nt, 4nt, 6nt, 8nt and 10nt, respectively. *P < 0.05 by one-sided Student’s t test. f Representative gene ontology items of transcripts with cold-responsive RG4s.
