Figure 5. The MHC II Locus Is Found within Other CTs upon IFN-γ Activation.

(A and B) A BAC probe for the MHC II locus (red) was cohybridized with a Chromosome 6 paint (green) in cryosections of control and IFN-γ activated MRC5 human lung fibroblasts (nuclear edge outlined by dotted line). Insets show the position of the MRC II locus (arrows) in relation to its CT (in gray scale) (A). The positions of the MRC II loci were scored into four different categories. Loci found “inside” or “looped out” were easily classified; loci near the edge of the CT were divided into “inner edge” and “outer edge,” depending on whether they appeared more internal or external in relation to the remainder of the CT. Upon IFN-γ activation, the MHC II locus relocates to a more external position in relation to its CT, when compared with control cells (B, p = 0.02, two-tailed χ ² test, n = 118 and 117 loci for control and IFN-γ activated cells, respectively), as described before [ 27]. Note that due to the flatness of fibroblast cells, nuclear profiles from random sections are often elongated.

(C–E) The MHC II BAC probe (red) was cohybridized with paints for Chromosomes 1 (C, green), 2 (D, green), 8, or 9 (not shown) and the number of MHC II loci found within each of these CTs was scored in both control and IFN-γ activated cells (E). Upon activation, the MHC II locus is more likely to be found within one of Chromosomes 1, 2, or 9, when compared with control cells ( p = 0.038, two-tailed Fisher's exact test using pooled data from the three chromosomes), whereas no difference in association is detected if Chromosome 8 is included in the analysis ( p = 0.052, two-tailed Fisher's exact test using pooled data from all four chromosomes).