Identification of candidate cis-elements in the mouse Runx1 locus. (A) Gumby output and DHS (Chr 16: 92473100–92743100 spanning Runx1 plus 30 kb upstream and 15 kb downstream; NCBIM build 36). (i, top) Position of Runx1 exons (numbered according to Levanon and Groner⁶ ; coding sequence [dark blue], UTRs [light blue]). Gumby-identified CNEs (pink) and exons (blue) are shown as colored bars. Height of bars shows -log₁₀(P value) (cutoff at 10). (ii) Hematopoietic DHS detected along the mouse Runx1 locus (vertical red bars) in the area analyzed (horizontal black lines). Only 3 CNEs with a -log₁₀(P value) more than 10 corresponded to a DHS (light gray shading; P1 CNE not visible on this scale, Table S1). (B) Southern blots for P1, + 23, and P2 DHSs in E12 FL and 416B (nuclei treated with increasing concentrations of DNAseI [triangles]). G indicates genomic control; 0^ice, DNaseI free ice; and 0³⁷, DNAse I free 37°C controls. Restriction maps (to scale) with positions and sizes of probes (-) and DHSs () are shown next to each set of blots. DHS mapping to the P1, + 23, and P2 CNE are indicated. Additional DHSs (not discussed in this paper) are labeled a-d. X indicates XbaI; RI, EcoRI; and RV, EcoRV.