Figure 3.

Defining the PRDM9Cst binding sites of Esrrg-1 and Psmb9. (A) Scheme of Esrrg-1 hotspot with polymorphisms between C57BL/6J (B6) and CAST/EiJ (CAST) and amplicons for initial testing of PRDM9Cst binding. The red line represents the only fragment showing binding at this hotspot. (B) Esrrg-1 specifically binds to PRDM9Cst but not PRDM9Dom2 and competes with the other PRDM9Cst-dependent binding sites. The compositions of the binding reactions are shown above each lane. Red arrow, shifted band; black arrow, unbound fragment. (C) Detailed mapping of the Esrrg-1 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) Scheme of Psmb9 hotspot with polymorphisms between B6 and CAST, and amplicons for initial testing of PRDM9Cst binding. The approximate position of the Psmb9 binding site was reported previously [19], and therefore only three amplicons surrounding it were tested. Only the middle fragment showed binding to PRDM9Cst. (E) Psmb9 specifically binds to PRDM9Cst but not PRDM9Dom2 and competes with the other PRDM9Cst-dependent binding sites. The compositions of the binding reactions are shown above each lane. Red arrow, shifted band; black arrow, unbound fragment. (F) Detailed mapping of the Psmb9 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. (G) Sequences of the Esrrg-1 and Psmb9 minimal binding sites aligned with the inferred PRDM9Cst binding motif. The strong matches of the binding sites to the motif are in red.

Billings et al. Genome Biology 2013 14:R35   doi:10.1186/gb-2013-14-4-r35
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