Figure 3.

Influence of modulated random collision frequencies on long-range interactions and mammalian genome evolution. (a) Separation distances between conserved sequences (cs) and transcription start sites (TSS) of co-expressed mouse genes were determined as explained in the Materials and methods section. Black triangles depict the relative count of separation distances obtained for each supranucleosomal domain. Black squares indicate the mean of relative counts obtained from 30 random samples of genes. Error bars represent the 95% confidence intervals for randomization. Separation distances are significantly over-represented in domains III and V (+7.9% and +6.6%, respectively) while they are significantly under-represented in domain IV (-8.6%) (P-values of t-tests are indicated on the graph). (b) Histogram depicting the relative counts of cis-interactions in human GM06990 or K562 cells (Hi-C experiments from [4]) occurring in Giemsa-negative (gene-rich regions, white bars) or Giemsa-positive (gene-poor regions, gray bars) bands. For each set, the number of interactions was counted in each supranucleosomal domain (as defined in Figure 2a). Counts in each domain were normalized against the total number of sequence-tags counted over all domains (D.I to D.VI). Error bars represent standard error of the mean of two Hi-C experiments. The P-value indicated on the figure was obtained from a t-test (double asterisks indicate a P-value < 0.05 and >0.01, and triple asterisks a P-value < 0.01).