Normalized Capture-C counts using tsh (left) or tio (right) promoters as baits, indicated by the vertical colored lines (cyan, magenta). Capture-C was performed on wild-type embryos (control, black) and on embryos with deletion of the tio TSS/promoter (second track), deletion of the middle loop anchor (LA) (third track), deletion of the tio LA/3 UTR (fourth track), and with the middle LA replaced with a boundary (BND) insertion (lower track, orange). Zoom-in (underneath) indicates the location of the deletions/substitution (DEL/SUB) relative to the genes (blue) and the Capture-C probes (black, orange, cyan, magenta) at the three LAs. Deletion of the tsh LA abrogates the outer loop (fourth track, arrow). Replacement of the middle LA with a boundary (BND) leads to differential contact frequencies either side of the insertion, indicated by the horizontal lines (lower, orange).
