Fig. 3

VANC21-binding motifs and their distribution among VANDAL families. a DNA sequence motif most commonly found at FLAG-VANC21-binding sites in VANDAL21 TEs. Localizations of the motif are shown in Fig. 2b and Supplementary Fig. 6, with green and orange bars indicating positions of the C-type (“YAGTATTAC”) and T-type (“YAGTATTAT”) motifs, respectively. b Electrophoretic mobility shift assay (EMSA) by VANC21 protein for double-stranded DNA of the sequences shown in c. The probe sites are also shown by white arrowheads in Fig. 2b. 1*, 2*, and 3* have single-base substitutions within the motif relative to the original sequences. 4 and 5 are control sequences from the exons, where VANC21 localization was not detected. Results for dependence of the shift to the protein amount and a competition assay are shown in Supplementary Fig. 7. c Sequences of the dsDNA probe used in EMSA (b). d Numbers of C- and T-type motifs within VANDAL21 and related VANDAL family members within the genomes of A. thaliana and A. lyrata. A. lyrata-specific lineages are shown with red lines. IDs for these TE copies and bootstrap probabilities are shown in Supplementary Fig. 8c