Mapping the PRDM9Dom2 binding site of Pbx1. (A) Scheme of Pbx1 hotspot with polymorphisms and amplicons for initial testing of PRDM9Dom2 binding. The red line shows the position of the single binding site detected at this hotspot. (B) Pbx1 specifically binds to PRDM9Dom2 but not PRDM9Cst. The compositions of the binding reactions are shown above each lane. Red arrow, shifted band; black arrow, unbound fragment. (C) Detailed mapping of the Pbx1 binding site. The compositions of the binding reactions are shown above each lane. For the sequences of the competitor oligos used for final mapping, see Additional file 11 (Additional experimental procedures). Red arrow, shifted band; black arrow, unbound fragment. (D) The sequence of the 34 bp oligo representing the minimal binding site is aligned to the inferred PRDM9Dom2 binding motif [6,21] and the zinc-finger array of PRDM9Dom2 (amino acids at positions -1, 3, and 6 relative to the α-helix of each finger are shown). The strong matches of the binding site to the motif are in red.
Billings et al. Genome Biology 2013 14:R35 doi:10.1186/gb-2013-14-4-r35