Random collision frequencies at five mouse gene-rich loci. (a) Maps of mouse loci investigated. Genes are indicated by full boxes and promoters by thick black arrows. The scale bar indicates the size of 10 kb of sequence. The names of the loci and chromosomal location are indicated above each map. The HindIII (Usp22, Emb, Lnp, Mtx2 and 11qA5 gene-desert loci) or EcoRI (Dlk1 locus) sites investigated are indicated on the maps. Arrows indicate the positions of the primers used as anchors in 3C-qPCR experiments. (b) Random collision frequencies at five mouse gene-rich loci. Locus names are indicated above each graph. Random collision frequencies were determined by 3C-qPCR in the 30-day-old mouse liver at the indicated anchor sites (for further details see Materials and methods). They were determined in three independent 3C assays each quantified at least in triplicate and the data were normalized as previously described . Error bars are standard error of the mean of three independent 3C assays. Grey circles, triangles or squares are data points obtained from distinct genomic sites as indicated on the graphs. In each graph, red squares represent the floating mean (20-kb windows, shift of 10 kb). P-values (Mann-Whitney U-test) account for the significance of the differences observed between the higher and the lower points of the floating mean. They were calculated from the values of the average random collision frequencies in a window of 30 kb around these points (values indicated in the figure) (One asterisk indicates a P-value < 0.1 and > 0.05; double asterisks a P-value < 0.05 and > 0.01 and triple asterisks a P-value < 0.01).
Court et al. Genome Biology 2011 12:R42 doi:10.1186/gb-2011-12-5-r42