Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

K88N mutation significantly increases CRX HD's cooperative binding and transactivation activity on BAT-1 sequence containing a P3 dimeric HD motif. (A) Diagrams depicting K₅₀ HD preferred monomeric and dimeric P3 motifs. (B) Alignments showing WT BAT-1 probe sequences and variants. The P3 dimeric HD motif and four monomeric HD core motifs 5′-TAAT-3′ are labeled. (f) the core motif is on the forward strand; (r) the core motif is on the reverse strand. In BAT-1 variants, the mutated nucleotides are italicized and underlined. (C,D) EMSA gel images showing increasing amount of WT or K88N HD peptides bound to a fixed amount of BAT-1 (WT) or P5 GA control probes. The diagram, below each gel image shows the dimeric HD motif configuration and is labeled with the spacer length. (E) Schematics and barcharts of luciferase reporter assays comparing CRX WT and K88N transactivation activity at BAT-1 and variant enhancer sequences. Bars represent the mean. P-values of one-way ANOVA are annotated: (ns) >5 × 10⁻², (***) ≤1 × 10⁻³.