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Additional file 6 Table S3. Nucleus-by-nucleus analysis of pairs of allele conformations and of the effects of LPS/IFNγ activation.

Additional file 1 Fig. S1. BAC probe specificity control by 2D-FISH on porcine metaphases. (a) class I (SLA-1, SBAB-490B10) in green; class II (SLA-DRA, SBAB-591C4) in red; and class III (TNFα, SBAB-493A6) in yellow. (b) porcine chromosome 7 centromere in red (SBAB-437A9). (c) BAC probe specificity control by 2D-FISH on human metaphases: class I (HLA-A, RP11-192H11) in green; class II (HLA-DRA, RP11-379F19) in red; and class III (TNFα, RP11-184F16) in yellow.

Additional file 3 Fig. S2. 3D BAC center-to-center distances in resting and activated swine macrophages. Cumulative frequency graphs of the normalized center-to-center distances between: (i) MHC class III (TNFα) and SSC7 centromere in red; (ii) MHC class II (SLA-DRA) and SSC7 centromere in green. Pairwise comparisons (p-values) of cumulative 3D distance distributions in resting and activated macrophages (Student’s t-test) are indicated in each graph.

Additional file 4 Table S2. Comparison of gene expression level in resting macrophages. mRNA expression level, analyzed by RT-qPCR, were pairwise compared with one-way ANOVA model with repetitions.

Additional file 5 Fig. S3. Schematic representation of the method used to define the conformation of each allele: given that r1 and r2 are the radii of two fluorescent spots, when the 3D distance between two spot centers (d1) is greater than r1 + r2, the allele is assumed to be decompacted (D), whereas when the 3D distance (d2) between two spot centers is less than r1 + r2, the allele is assumed to be compacted (C).

Additional file 2 Table S1. Mean values of 3D normalized center-to-center distances and angles calculated using center-to-center distances.

Additional file 7 Fig. S4. Schematic representation of genes positioned inside survival zones (SZ) as determined by the application of the three-loci algorithm. The probable positioning of three genes (blue, red and green dots) is represented in two cells as an example (in cell 1 shown by dotted lines, and in cell 2 by continuous lines). The different positions of each gene make it possible to define its SZ represented by a circle of the same color. The radius of the circle defined for each locus is denoted by Rb for the blue dot, Rr for the red dot and Rg for the green dot.

Analysis of the interaction between IGF2-DLK1 and IGF2-MEG3 RNAs in muscle cells. Decomposed confocal images and merge showing RNA hybridization signals for: a, I: IGF2 (red), II, DLK1 (green) RNAs and III merge; b, I: MEG3 (red), II: IGF2 (green) RNAs and III merge. White arrows on merge images indicate colocated RNAs. The nucleus is counterstained with DAPI (blue). (PPTX 636 kb)

a, Distribution of DNA spot centers to CT edge distances for both alleles located outside of CT is shown. For both alleles, the maximal distance found between RNA spot center and CT edge reached 2 μm. No statistically significant difference was found between the two alleles; however the distribution shows a tendency of the expressed allele to be more frequently outside the CT; b, Heat map representing the position of pair of alleles in each nucleus. The position of each allele towards its CT is analyzed within the 9 different combinations of position. No statistically significant difference was found (n = 51 nuclei). (PPTX 84 kb)

IGF2 - (DLK1-MEG3) DNA positioning relative to CTs (SSC2 and SSC7) in liver cells. Two examples (a, b) of decomposed confocal images showing 3D DNA FISH of IGF2 and DLK1/MEG3 loci in an undifferentiated color (white) (I) and merge (II) with specific chromosome painting probes (SSC2 in red and SSC7 in green). White arrows on merge images indicate the position of proximal alleles. The nucleus is counterstained with DAPI (blue). (PPTX 540 kb)

a, Distribution of DNA spot centers to CT edge distances for both alleles located outside of CT is shown. For both alleles, the maximal distance found between RNA spot center and CT edge reached 2 μm. No statistically significant difference was found between the two alleles; however the distribution shows a tendency of the expressed allele to be more frequently outside the CT; b, Heat map representing the position of pair of alleles in each nucleus. The position of each allele towards its CT is analyzed within the 9 different combinations of position. No statistically significant difference was found (n = 51 nuclei). (PPTX 84 kb)

Information on the genes studied and mapping results in pig. (DOCX 16 kb)

Analysis of the interaction between IGF2-DLK1 and IGF2-MEG3 RNAs in muscle cells. Decomposed confocal images and merge showing RNA hybridization signals for: a, I: IGF2 (red), II, DLK1 (green) RNAs and III merge; b, I: MEG3 (red), II: IGF2 (green) RNAs and III merge. White arrows on merge images indicate colocated RNAs. The nucleus is counterstained with DAPI (blue). (PPTX 636 kb)

IGF2 - (DLK1-MEG3) DNA positioning relative to CTs (SSC2 and SSC7) in liver cells. Two examples (a, b) of decomposed confocal images showing 3D DNA FISH of IGF2 and DLK1/MEG3 loci in an undifferentiated color (white) (I) and merge (II) with specific chromosome painting probes (SSC2 in red and SSC7 in green). White arrows on merge images indicate the position of proximal alleles. The nucleus is counterstained with DAPI (blue). (PPTX 540 kb)