Figure S9. Enrichment in transcription factor binding sites and distribution of TE superfamilies at MED14- and UVH6-dependent loci.

(A–C) TF binding sites showing significant enrichment at the indicated gene sets relative to random sets of the same number of genes (two-sided two proportion Z-test, P-value Bonferroni adjusted <0.05 and −log10 [P-value] >2). The number of genes containing binding sites for the corresponding TFs are indicated in white. TF binding site data were retrieved from published datasets (O’Malley et al, 2016). (D) Reads per kilobase per million mapped reads (RPKM) log₂ values in the WT (L5 background) at 37°C, med14-3 at 37°C (left) and uvh6-3 at 37°C (right) of TEs up-regulated in heat-stressed WT plants. (E) Relative frequency of TE superfamilies in the Arabidopsis genome (TAIR10, white) and the following datasets: TEs up-regulated in WT plants subjected to heat stress (red), among these, TEs down-regulated in med14-3 at 37°C (dark blue) or in uvh6-3 at 37°C (green) relative to the WT at 37°C.