Supplementary Figure 8: Corroboration of CHi-C interactions.
From: Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
The promoter interaction map shows the promoter interaction profiles of (a) BCL6, (b) HOTTIP, (c) TMEM159, (d) SOX4 and (e) RFC3. The size and color of each interaction peak reflect the relative number of reads per fragment. ChromHMM functional annotation tracks are displayed below the interaction profiles. Graphs show the gel quantitation of interactions by 3C between the promoter fragment and non-interacting fragment (prom-neg; black columns) and between the promoter fragment and interacting fragment (prom-elem; gray columns). L, DNA ladder; Co, PCR control. Asterisks denote PCR primer positions. For BCL6, interactions were also assessed by three-dimensional DNA FISH, using BAC probes encompassing the BCL6 promoter (green, G) and non-interacting (purple, P) and +1.2-Mb interacting (red, R) regions, shown as bars below the map. Representative examples of signals in GM12878 and CD34+ cells are shown. The outline of DAPI counterstaining is shown as a dotted white line. Graphs show measurement of the distance between signals (green-red, GR; green-purple, GP; purple-red, PR); the number of loci analyzed is shown (n).
