Fig. 3

Changes in H4K16ac epipolarity are linked to the changes in chromosome 11 homologs distribution. a Comparison of the observed peak count and expected peak count relative to the chromosome size for the 118 peaks identified as described in panel M. Goodness of fit test was used, and it revealed that these 118 differentially bound H4K16ac peaks are not randomly distributed and chromosome 11 presented with the highest enrichment score. b Representative confocal 3D reconstruction of the nucleus (stained with DAPI, blue) and of chromosomes 3 (red), 7 (green), and 16 (green) by FISH stained with full-paint probe in young and aged HSCs. Bar = 2 μm. c Measurements of the distances between chromosomes 3 (n = 3 biological repeats, 28 cells for young, 21 cells for aged in total), 7 (n = 3 biological repeats, 25 cells for young, 26 cells for aged in total), and 16 (n = 3 biological repeats, 30 cells for young, 18 cells for aged in total) homologs in young and aged HSCs by Volocity 3D Image Analysis Software. d Percentage of young and aged HSCs with chromosome homolog proximity for chromosomes 3, 7, and 16, n = 3 biological repeats. e Representative confocal 3D reconstruction of the nucleus (stained with DAPI, blue) and of chromosome11 (red, FISH stained with a full-paint probe) in young, aged, and aged+CASIN 5 μM HSCs. Bar = 2 μm. f 3D reconstruction of the chromosome 11 homologs (red and green) and the distance measurement between them by Volocity 3D Image Analysis. In young HSCs, green color for two homologs shows that they are distributed very close to each other and are not recognized as two objects by the software. While in aged and aged+CASIN 5 μM HSCs, they are marked as two objects in green and red. Bar = 2 μm. g Measurements of the distances between chromosome 11 homologs by Volocity 3D Image Analysis. Shown are mean values + 1 SE; *p < 0.01; n = 6 biological repeats, 64 cells for young, 58 cells for aged, and 55 cells for aged+CASIN in total. h Percentage of young, aged, and aged+CASIN 5 μM HSCs with homolog proximity for chromosome11; **p < 0.01. i Representative confocal 3D reconstruction of young, aged, and aged+CASIN 5 μM HSCs after DNA-FISH+IF. H4K16ac (green), chromosome 11 (red), the nucleus is stained with DAPI (blue). Bar = 2 μm. j Volume measurement of the co-localized area between H4K16ac and chromosomes 11 and 16 by Volocity 3D Image Analysis; *p < 0.05, n = 3 biological repeats, 33 cells for young, 33 cells for aged, and 28 cells for aged+CASIN in total for chromosome 11 and 32 cells for young, 26 cells for aged, and 19 cells for aged+CASIN in total for chromosome 16