Table 2. TF Motifs Significantly Enriched in THSs in All Four Species.

TF	Family	Average Expression in Arabidopsis Root Tip (RPKM)	Percentage of Motif Occurrences in the Arabidopsis Genome That Overlap with a Known Binding Site	Percentage of Motif-Containing THSs in Arabidopsis That Overlap with a Known Binding Site (High-Confidence Binding Sites)
AT5G11260 (HY5)	bZIP	37	30.3% (7,156/23,541)	61.2% (810/1,323)
AT4G34000 (ABF3)	bZIP	1	53.3% (3,821/7,164)	97.1% (1,279/1,316)
AT4G25470 (CBF2)	AP2	16	64.2% (13,144/20,457)	89.1% (582/653)
AT3G50060 (MYB77)	MYB/SANT	6	52.5% (9,147/17,402)	74.6% (506/678)

THSs found in at least two replicates for each species were analyzed for overrepresented TF motifs. Four of the 30 TFs that were significantly enriched in THSs of all four species are shown in the table. Significant occurrences of each TF motif were identified across the Arabidopsis genome, and the percentage of these motif occurrences that fall within known binding sites for that factor (based on published ChIP-seq or DAP-seq data sets) are indicated in column 4. The final column indicates the percentage of Arabidopsis root tip THSs that contain a motif for each factor and also overlap with a known binding site for the factor. These are considered high-confidence binding sites (Supplemental Figure 4).