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Fig. 2 | BMC Genomics

Fig. 2

From: Single-molecule analysis of subtelomeres and telomeres in Alternative Lengthening of Telomeres (ALT) cells

Fig. 2

Subtelomeres with a high fraction of recombinant molecules. The hg38 subtelomere reference sequences are shown as light blue bars; the dark blue vertical ticks within these bars indicate in silico Nt.BspQI nick-label sites. The location of the telomere is shown with a red “T”. Representative examples of raw images of single molecules that were imaged are shown below the references. The DNA backbone is blue, and both the labeled subtelomeric Nt.BspQI sites and the telomere (TTAGGG) n tracts are green. a Chromosome 21q molecules with a defined pattern in the recombination partner. The top U2OS molecule shows 21q with an end telomere. The second and third U2OS molecules are examples of 21q end recombination with retention of an internal telomere-like sequence (ITS). The bottom two U2OS molecules show the same recombination event but lack a detectible ITS. The top Saos-2 molecule shows 21q with an end telomere. b Chromosome 9p molecules from U2OS without a defined pattern in the recombination partner. Chromosome 7q molecules from SK-MEL-2 without a defined pattern in the recombination partner. Individual single-molecule maps were de novo assembled into the consensus maps (yellow lines), which were then aligned with the hg38 reference (light blue bars). The green lines on the consensus maps are Nt.BspQI (GCTCTTC) sites that align to the corresponding reference site. Those that do not align with the reference are designated with light blue lines. The top U2OS molecule shows a structural variant of the 9p end with an end telomere. The bottom two U2OS molecules show the same structural variant of the 9p end following recombination resulting in two distinct partner fragments, with retention of ITSs in both cases. Likewise the top 7q SK-MEL-2 molecule has an end telomere while the bottom two show recombinants with ITS retention

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