Fig. 1: Identification of a distal limb bud-specific enhancer.

a ATAC-seq profile (top) and binding profiles of the HOXA13 (middle) and HOXD13 (bottom) transcription factors by CUT&RUN, using E12.5 wild-type distal forelimb cells, covering the entire HoxD locus, including the two flanking TADs C-DOM and T-DOM (mm10 chr2:73950000-75655000). Green rectangles below are distal limb enhancers in C-DOM and orange rectangles are proximal limb enhancers in T-DOM. The Hoxd gene cluster is indicated at the center (the 5′ to 3′ direction of transcription is indicated by a black arrow) and the Lnpk and Mtx2 genes are indicated as rectangles with black borders. The Hoxd13 gene is on the centromeric end of the cluster and indicated by a purple rectangle with a circle on top, whereas Hoxd1 is telomeric and indicated by a square top. The C-DOM Island II enhancer¹⁷ is a green rectangle with a black border and its corresponding signal peaks are surrounded by a dashed vertical box. b Magnification of the same tracks as above centered around the Island II enhancer with the H3K27ac ChIP-seq signal (top) in E12.5 distal forelimbs²³. The overlying profiles indicated by dark gray lines are from ChIP-seq using E11.5 whole limb buds²⁵ and are shown for comparison. Below the CUT&RUN profiles are the MACS2 peak summits for the corresponding CUT&RUN samples. The green rectangles below indicate regions described as Island II in¹⁷ or in²⁷. The Del II1 shows the region deleted in this work (Supplementary Fig. 1-2) and II1 TgN is the transgene used panel in the next panel. c LacZ staining pattern produced by the II1:HBB:LacZ (II1 TgN) enhancer reporter transgene at E12.5, showing high specificity for distal limb cells (top). Below are whole-mount in situ hybridizations for Hoxa13 and Hoxd13 in wild-type E12. 5 forelimbs for comparison. Scale bars are 0.5 mm.