Tracing PGP1f chromosomes.

(A) OligoSTORM image of a diploid nucleus showing CS1-9 (Bottom, rounds 1 through 9; 1.28, 1.24, 1.80, 1.04, 0.56, 0.52, 0.84, 0.52, and 0.36 Mb, respectively) and four subregions of CS7 (top, rounds 10 through 13; 140, 260, 350, and 90 kb, respectively) of both homologs. In this and all panels excepting F, radius of spheres represents the localization precision in the axial dimension. Note, the coordinates of the four subregions, selected based on the IMR-90 Hi-C map, correspond well to contact domains. Sequencing depth of the PGP1f Hi-C map was not, however, able to confirm these as contact domains in PGP1f, and thus they are referred to simply as subregions. (B) Same as in A with respect to CS1-9, but a different nucleus. (C) Loop (290 kb), including loop anchors (rounds 14 and 16; pink and orange; 10 kb each) and loop body (round 15; blue; 270 kb); *, we also imaged the upstream and downstream regions flanking the loop (rounds 17 and 18; 20 and 80 kb, respectively), but these are not shown so that the structure of the loop can be more apparent. (D) DNMT1 gene (round 19; 59.5 kb) and its DMR (round 20; 2.9 kb). (E) Walking along chromosome 19 in variable step sizes (see A) while also walking along chromosomes 3 and 5 in uniform step sizes (500 and 250 kb, respectively). (F) OligoDNA-PAINT images of CS7-9 of one homolog showing each chromosomal segment by itself (top; color scale represents depth in z) or merged (bottom; color scale represents different chromosomal segments). In contrast to other panels, localizations are blurred according to precision. (G) Superimposition of two images, taken 90 hours apart, each of both homologs of CS1 in (red, first image; blue, later image). Average overlap is 80 ± 9% and 68 ± 12% (n = 20) when images are aligned based on their centers of mass (left) or not (right), respectively. (H) Superimposition of two images from one nucleus of both homologs of CS7, one image encompassing all of CS7 (blue) and the other being a composite of the four subregions (green; 140, 260, 350, and 90 kb) comprising CS7. With alignment based on centers of mass, 85% of the single image overlapped the composite image, and 76% of the latter overlapped the former (left). Without alignment, the analogous values were 84% and 75% (right).