Figure 2

Defining the PRDM9^Cst binding site of Hlx1. (A) Scheme of Hlx1 hotspot with polymorphisms between the C57BL/6J (B6) and the CAST/EiJ (CAST) mouse strains (from Paigen et al. [5]) and amplicons for initial testing of PRDM9^Cst binding. The positions of single-nucleotide polymorphisms (SNPs) were taken from the National Center for Biotechnology Information (NCBI) build 37. The red line represents the only fragment showing binding at Hlx1. (B) Hlx1 specifically binds to PRDM9^Cst but not PRDM9^Dom2. The compositions of the binding reactions are shown above each lane. Red arrow, shifted band; black arrow, unbound fragment. (C) Detailed mapping of the Hlx1 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). (Left panel) Definition of the minimal binding site; (right panel) Strength of binding of PRDM9^Cst to B6 and CAST sequences of the Hlx1 binding site. Red arrow, shifted band; black arrow, unbound fragment. (D) Sequences of the Hlx1 minimal binding sites in B6 and CAST strains aligned to the inferred PRDM9^Cst binding motif. Sequence differences are underlined. The strong matches of the binding sites to the motif are in red. (E) Hlx1 competes with the other PRDM9^Cst-dependent binding sites. The compositions of the binding reactions are shown above each lane. Red arrow, shifted band; black arrow, unbound fragment.