5C array analysis of chromatin conformation changes in the HoxA cluster during cellular differentiation. HoxA chromatin contacts in undifferentiated cells are presented as a two-dimensional heat map. Pair-wise interaction frequencies between restriction fragments were detected by 5C and measured on custom microarrays. A linear diagram of the HoxA gene cluster is presented at the top and right borders and is as described in Figure 2b. A predicted BglII restriction pattern is illustrated below the HoxA diagram and is to scale. Restriction fragments were identified from left to right by the numbers indicated below each line. Intersecting column and row numbers identify DNA contact. Values within each square represent interaction frequencies and are color-coded. The color scale is shown in the bottom left inserts, with pale yellow to brown indicating very weak to strongest contacts. Interaction frequencies are the average of at least three array technical repeats. Note: primer 48 was included during large-scale 5C library production but was excluded from our analysis because of homology to repetitive sequences.
Fraser et al. Genome Biology 2009 10:R37 doi:10.1186/gb-2009-10-4-r37