Figure 1.

The transcriptionally silent HoxA cluster is organized into multiple chromatin loops in the human genome. (A) Linear schematic representation of the HoxA cluster on human chromosome 7. Predicted BglII restriction fragments are identified from left to right by numbers. (B) 3C interaction frequency heat map of the silent HoxA cluster. Pair-wise interaction frequencies were measured by 3C in undifferentiated NT2/D1 cells. Intersecting column and row number identifies DNA contact corresponding to interaction frequency. Interaction frequencies are color-coded based on the scale presented on the left. Genomic regions involved in looping interactions are highlighted by shaded boxes. Additional information about this data set is available on our website (‘Materials and Methods’ section). (C) Two-dimensional schematic representation of the silent human HoxA cluster in vivo. Schematic is not to scale to enable two-dimensional illustration of DNA contacts. Yellow circles highlight an area encompassing strongest looping contacts in the cluster rather than the actual number of interactions.