siRNA–targeting of VarTEs and the effect on proximal gene expression.
(a) Upper panel depicts siRNA-targeting of variable and invariable regions of VarTEs defined between Col-0 and Bur-0 or C24. Lower panel shows abundance of Col-0 siRNA in siRNA+ InvTEs (red) and siRNA+ VarTEs (yellow) between Col-0 and Bur-0 or C24. Within siRNA+ VarTEs, the abundance of Col-0 siRNA was compared between invariable (cyan) and variable regions (navy). MWU [InvTE/VarTE] p<2×10−16 for Col-0 versus Bur-0/C24. MWU [variable/invariable regions of VarTEs] p[Col-0/Bur-0] = 1×10−5, p[Col-0/C24]<2×10−16 (b) VarTE+ genes were divided into subgroups based on whether the closest proximal TE was siRNA− (cyan), InvsiRNA+ (dark gray) or VarsiRNA+ (light gray). The average expression level of each gene group is shown. MWU [siRNA− VarTE+/InvsiRNA+ VarTE+] p[Col-0/C24] = 0.01, p[Col-0/Bur-0] = 0.01; MWU [siRNA− VarTE+/VarsiRNA+ VarTE+] p[Col-0/C24] = 9×10−5, p[Col-0/Bur-0] = 0.003; MWU [VarsiRNA+ VarTE+/InvsiRNA VarTE+] p[Col-0/C24] = 0.01, p[Col-0/Bur-0] = 0.04; * = p<0.05, ** = p<0.01. Standard errors are shown.