Physical interactions within the Krox20 locus.

(A) Alignment of data in the Krox20 and adjacent loci from Hi-C in ES cells [11], 4C-seq in E9.5 whole mouse embryos, using the Krox20 and Nrbf2 promoters as viewpoints (this work, 2 biological replicates) and CTCF ChIP-seq in E14.5 mouse brain (ENCODE, [58]). (B) Zoom in on the Krox20 locus, showing 4C-seq data from the Krox20 promoter, element A, element B and element C as viewpoints. CTCF ChIP-seq data in E14.5 mouse brain (ENCODE) are indicated below. Signals from simultaneously processed E9.5 whole embryo (dark blue) and E8.5 embryo head (light blue) samples are shown. On the right, normalized distributions of the 4C-seq signals in different genomic regions are indicated. TADs as defined in [7] or by our additional analysis (S2 Fig) are indicated above, with dashed lines in the graphs demarcating TAD boundaries. Genes (black/red), cis-regulatory elements (orange) and genomic coordinates are indicated below each set of data. Arrowheads above each 4C track pinpoint viewpoints.