Figure 3

Specific energies of interaction and associated chromatin factor contacts. Shown in (A, B, C) are the energies of interaction \(\delta F_{i,j} = F_{i,j} - \bar {F}_{j-i}\) of a portion of chromosome 2L for three different F _i,j matrices: A) raw, B) raw + PC filtered and hierarchical. (The first 35 PCs were used in reconstructing the raw + PC free energies). All have been aligned so that the zeroth column corresponds to i=j. Blue regions correspond to attractive interactions (negative) and red regions to effective repulsive interactions (positive). Figures (D, E) show the locations of pairwise self contacts, \(S_{i}^{\mu } S_{j}^{\mu }\) for the insulator factor BEAF and the polycomb group protein Pc (blue corresponds to \(S_{i}^{\mu } S_{j}^{\mu } = 0\) and red to \(S_{i}^{\mu } S_{j}^{\mu } = 1\)). Comparing the interaction energies (A, B, C) with the locations of pairwise contacts (D, E) highlights how these contacts could be generating the observed interactions.