Fig. 3: Micro- and small-exon skipping in grp20 flowers and leaves, and RNA expression of floral homeotic and LOB ___domain genes.
a, Relative levels of alternative floral transcripts with affected exons of floral homeotic genes and AS2 in different genotypes (shown as mean ± s.e. from three biological replicates). The P value is shown in the following order (from left to right) in a and j by two-sided Student’s t-test, **indicate P < 0.01 and NS indicates not significant: WT versus GRP20, WT versus grp20-1, WT versus GRP20 (RBDm) and WT versus GRP20ΔHDR. For AP1, P = 0.13, 1.9 × 10−5, 0.0005 and 0.0026; for SEP4, P = 0.16, 0.00017, 0.003 and 0.0013; for AG, P = 0.37, 0.002, 0.024 and 0.00056; for STK, P = 0.12, 0.00058, 0.0029 and 0.00017; for AP3, P = 0.32, 0.0003, 0.0064 and 3.5 × 10−5; for PI, P = 0.09, 0.0039, 0.0081 and 0.00037; for AP2, P = 0.11, 0.00041, 3.4 × 10−5 and 0.0017; for AS2, P = 0.92, 0.0028, 0.0027 and 0.00086. For primer information, see Extended Data Fig. 3 and Supplementary Table 7. b,c, The length distribution of skipped exons and all exons in the genes in flowers (b) and leaves (c), with two-sided Student’s t-test. The lower bound, maxima, minima, centre and upper bound of box plots (from left to right) are shown as follows: for skipped exon in b: 40, 2,131, 2, 48 and 88.5; for all exons in b: 48, 2,131, 2, 151.56 and 247.26; for skipped exon in c: 61, 2,757, 5, 83 and 131; for all exons in c: 93, 2,757, 5, 169.29 and 286.13. d,e, Venn diagrams for overlaps for 238 skipped exons in grp20 flowers (d) or 265 skipped exons in grp20 leaves (e), with exons of various size ranges. f, The enrichments were indicated by two asterisks as the fraction of skipped exons larger than twice the corresponding referenced exons. Fractions of exon numbers in various size ranges to total exons (reference) and skipped exons in various size ranges to total skipped exons in grp20 flowers and leaves. g, Two asterisks indicate enrichments that the fraction is larger than 0.0025. Fractions of skipped exon numbers to total exons in various size ranges in grp20 flowers and leaves. h, GO category analysis of genes with affected micro-exon skipping in grp20 flowers and leaves, shown for those with P < 0.05 (Mann–Whitney U test with 95% confidence intervals). i, Illustrations of AP3, AP2 and LBD2 gene structures with positions of forward (F) and reverse (R) primers for qRT-PCR of specific transcripts. Blue boxes, exons; thin lines, introns; orange boxes, wild-type micro exons; red boxes, skipped micro exons in AP3 and AP2. A green box in LBD2: an alternative extra exonic region (A5SS) in LBD2. The red dotted boxes below gene structures are enlargements of the affected regions of AP3 and AP2; dashed lines, introns and the skipped micro exons; thick pink line below each gene structure, the region as control for amplifying both wild-type and alternative transcripts. j, Relative expression of AP3 and AP2 transcripts with micro-exon skipping, or alternative 5′ site in LBD2, in flowers by RT-qPCR. For AP3, P = 0.83, 4.14 × 10−6, 0.00041 and 6.4 × 10−6; for AP2, P = 0.9, 3.31 × 10−5, 8.01 × 10−6 and 3.46 × 10−7; for LBD2, P = 0.22, 0.00083, 0.0011 and 5.49 × 10−5. The data are presented as mean ± s.e.m. from three biological replicates for a and j.
