Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations

HOXD13^Q317K binding, but not HOXD13^Q317R, acquires PITX1-like properties. (A) Coverage profiles for HOXD13^wt, HOXD13^Q317R, HOXD13^Q317K, and PITX1 in a 20-kb region covering the MGP gene show the similarity in binding between HOXD13^Q317K and PITX1. (B) MGP is threefold up-regulated in PITX1- and Hoxd13^Q317K-infected chMM cultures and threefold down-regulated in Hoxd13^wt cultures (log₂ fold changes compared to mock-infected cultures). (C) Peak overlap with respect to HOXD13^wt and PITX1 peaks. (Left) PITX1 shares 1.0% (383/40,881) of its peaks with HOXD13^wt; 27.5% (5887/21,396) with HOXD13^Q317R; and 6.0% (1492/25,036) with HOXD13^Q317K. (Right) HOXD13^wt shares 1.1% (383/34,267) of its binding sites with PITX1; 3.0% (633/21,396) with HOXD13^Q317R; and 6.7% (1671/25,036) with HOXD13^Q317K. (D) HOXD13^Q317K shares binding properties with both HOXD13^wt and PITX1. Mean read densities centered (±3 kb) around the peak summits for HOXD13^wt, HOXD13^Q317R, HOXD13^Q317K, and PITX1 (left to right). HOXD13^wt (164.1 tags/50 bp; 93.5 tags/50 bp; 43.2 tags/50 bp; 23.6 tags/50 bp), HOXD13^Q317R (49.7 tags/50 bp; 101.2 tags/50 bp; 49.8 tags/50 bp; 19.5 tags/50 bp), HOXD13^Q317K (24.9 tags/50 bp; 51.9 tags/50 bp; 109.1 tags/50 bp; 25.6 tags/50 bp), and PITX1 (15.1 tags/50 bp; 24.2 tags/50 bp; 38.9 tags/50 bp; 191.2 tags/50 bp).