To distinguish between the direct inhibition through the α C-terminus and the indirect inhibition through competition for DNA binding sites, we repeated these experiments with DNA-binding domutantstants of both ΔN forms.
To ascertain that the inability of BH2 to replace tightly bound BH4 was not due to its inability to create a tight-binding site, we repeated the experiments of Figure 3B with 4-amino-BH4 instead of BH2.
For every binding site, we retrieved repeat-masked sequence and used de novo motif discovery algorithm MEME [26] to look for shared sequence motifs.
Although previously defined genomic sites contain multiple TAAT sequences with flanking bases distinct from those in the optimal binding site, we have found a new binding site with seven near-perfect repeats of the optimal sequence; this site is located in the promoter region of decapentaplegic, a probable Ubx regulatory target.
As such, they had to be mirrored; that is, the binding site is repeated immediately adjacent, but in the opposite strand orientation, to maintain the inverted repeat orientation (Fig. 2B).
To further investigate the sites lacking canonical binding sequences, we repeated the de novo motif analysis on only those sites without a CRE sequence match.
Indeed, an artificial DOF1 binding site repeated in single or multiple copies could not drive guard cell expression.
We sequentially deleted each of the AP-1-binding sites and repeated the luciferase assays.
In gelatinase subfamily of MMPs (i.e., MMP-2 and MMP-9), the catalytic domain that contains the Zn2+ binding site and repeats of fibronectin motifs allowing the ability to bind their major substrate gelatin.
In an attempt to discriminate between the occurrence of closely associated and directly overlapping binding sites for MEIS1 and NKX2-5, we repeated this analysis but restricted the comparison to a region of ±6 bp around the summit of the binding peaks identified in the different datasets.
