Fig. 10

Chromatin loops, CTCF binding and other features of the Pax6 locus. Genome browser representation of the loops (shown as arches) found at the Pax6 locus and its flanking regions in lens epithelium (red), lens fibers (blue) and ES (green) cells. Pax6 coding regions including both proximal 5’- and 3’-flanking non-coding regions are highlighted in yellow. Compartments A and B are shown by red and blue horizontal bars, respectively. TAD regions identified by “Arrowhead” are shown in green. Whole lens ChIP-seq (H3K27ac, H3K4me1, H3K4me3 and H3K27me3 [59] and RNA polymerase II (Pol II) [47] tracks using whole lens (WL) chromatin are also shown. A broad region of H3K27ac is marked by a horizontal bracket. Lens epithelium (epi) and fiber cell CTCF (present study), ES cell CTCF [66], and ATAC-seq [56] are shown together with ENCODE candidate cis-regulatory elements (cCREs): Promoter-like signatures (red), proximal enhancer-like signature (orange), distal enhancer-like signature (yellow), DNase-H3K4me3 (pink) and CTCF (blue). Specific CTCF peaks and loops discussed in the text are marked by dotted boxes (1–3), numbered arrows (4–6) and (L1-L4), respectively. Yellow box is used to indicate locus of interest and scale.