Supplementary Figure 1: Ihh interacts preferentially with its upstream neighboring gene Nhej1.

Genes are indicated by gray lines, and Ihh and Nhej1 are highlighted in blue. 4C–seq performed in E14.5 limbs using the Ihh promoter as the viewpoint is shown below. Note the increased interactions with intron 3 of the adjacent Nhej1 gene. The gray line indicates the zoomed region displayed in Figure 1. Black bars indicate the size and position of human duplications converted to mouse genome coordinates that overlap with the regulatory landscape of Ihh. Below, Capture-C data from Andrey et al. (2017) at different developmental time points. Chromatin organization is maintained during limb development.