Fig. 2

Gene repositioning relative to heterochromatin compartments. a Graphical summary of the experimental procedure with gene locus detected by 3D FISH depicted as red dots and heterochromatin compartments in green. The shortest 3D distances to the constitutive (chromocenters) and peripheral heterochromatin (black arrows) were measured and single cell normalized as described in the “Methods”. b Rationale and visual explanation of possible Pearson’s correlation coefficients (R) relating gene expression changes (up-regulated, down-regulated or no expression change) to changes (Δ) in gene locus proximity to heterochromatin (chromocenters at the left and periphery at the right). A positive correlation (R = 0 to +1) indicates movement to heterochromatin upon down-regulation or vice versa, confirming heterochromatin as a silencing compartment. A negative correlation means that genes move closer to heterochromatin upon up-regulation (or away upon down-regulation). A negative correlation (R = 0 to −1) does not support the hypothesis of heterochromatin as a silencing compartment. c Results of the correlation analysis of locus repositioning (relative to chromocenters and to the periphery, as indicated) versus changes in gene expression upon differentiation and ectopic MeCP2 expression. Expression changes (during myogenesis and upon ectopic MeCP2 expression) are correlated for mean normalized distances at different scales: gene locus of interest, whole BAC, 2- and 5-Mbp genomic domains centered around the gene of interest. *Significant correlation (p < 0.05) (Table 1)