Multiomic profiling of telomere-driven replicative crisis in human fibroblasts. (A) A schematic of the human MRC5 fibroblast model of telomere-driven replicative crisis and the high-throughput sequencing (HTS) data sets analyzed in this study. Untransformed and MRC5 transformed by retroviral transfer of human papillomavirus 16 (HPV) E6 and E7 (E6E7) oncogenes (Bond et al. 1999) were sampled for targeted capture sequencing, Circle-Seq (Møller 2020), Fusion-seq (Liddiard et al. 2016), Kas-seq (Lyu et al. 2022), and chromatin capture (Downes et al. 2022) sequencing as indicated. Transformed MRC5 (MRC5^E6E7) were cultured through replicative crisis toward growth arrest with DNA extracted at Early (23 population doublings [PD]), Deep (PD47), and Late (PD57) time points after the appearance of telomere fusions. (B,i) The proportions of genomic intervals derived from key data sets analyzed in this study that overlap with genomic features of interest. (Genes) Coding sequence, (FRA) fragile sites, (CenSat) centromere satellites, and (R-loops) three-stranded nucleic acid structures. Samples include a simulated data set of 1 million random genomic loci (random), telomere fusions sequenced from MRC5^E6E7 crisis cells (fusions), single-strand DNA (ssDNA) peaks determined by KAS-seq in Early (E) or Deep (D) crisis samples, chromatin capture (CC) data sets collected at Early (E) and Deep (D) time points using hybridization probes targeting the Chr17p (17pT) and ChrXpYp (XpT) telomere-adjacent sequence, and extrachromosomal circular DNA (eccDNA) from Untransformed (U) and MRC5^E6E7 cells at Early (E) and Deep (D) crisis stages. (ii) A principal component analysis (PCA) plot (Galaxy Community 2024) of an extended range of data sets reveals the clustering of these samples based on the variance of these core parameters (indicated in the table below). Samples are encoded as in i, with the inclusion of ssDNA peaks common to both Early- and Deep-crisis samples (Shared [S]), CC data sets from Early (E) and Deep (D) crisis stages generated using the noncoding ChrXp genomic locus hybridization probe (XpG), and eccDNA data sets exclusive to Untransformed MRC5 (UO) or crisis MRC5^E6E7 (E6E7) cells.