Extended Data Fig. 7: U2OS neotelomere validation.
From: Most large structural variants in cancer genomes can be detected without long reads
(a) Schematic of neotelomere detection assay. Genomic DNA was subjected to EcoRI digestion followed by Southern blotting with a radiolabeled probe to the site of a chr 10 GRTR+ loose end (bottom track). Alleles that lack a neotelomere at this location will show a focal ≈ 5 kbp control band. A neotelomere will yield a diffuse band that is sensitive to digestion by the exonuclease Bal-31 prior to EcoRI digestion. (b) A Southern blot shows a diffuse high molecular weight band in U2OS but not in a control cell line (SAOS-2), consistent with a neotelomere. Both cell lines show the ≈ 5 kbp EcoRI control band. (c) The U2OS-specific band disappears when double stranded DNA ends of intact genomic DNA are digested by Bal-31 for over 5 minutes prior to EcoRI digestion and probe hybridization, confirming a new chromosome end (left). Bal-31 digestion does not substantially alter the overall size distribution of ethidium bromide (EthBr) labeled DNA fragments in the EcoRI digest (right). Time refers to length of Bal-31 exposure. Experiment repeated three times with similar results. Panels show uncropped images of entire gel lanes.
