Abstract
Telomere-driven replicative crisis transforms the architecture of the evolving cancer genome, yet the mechanisms and consequences remain incompletely resolved, with potential biomarkers undiscovered. To address this, we have employed novel tools and methodologies to explore a human fibroblast model of crisis using high resolution multi-omics analyses. We have developed a unique chromatin conformation capture procedure for identifying distant genomic loci that interact with eroding telomeres, uncovering large-scale structural changes that accompany crisis transition. We reveal the remarkable shift from local to distant genomic interactions consistent with crisis-induced chromatin decompaction and altered gene expression. To resolve variation within challenging repetitive sequences disclosed in the complete telomere-to-telomere human reference, we designed a targeted capture panel, uncovering ageing signatures within centromeric sequences and gross copy number losses within ribosomal DNA tracks and near to the chromosome ends. We have employed both short- and long-read sequencing of purified extrachromosomal circular DNA to expose an unequivocal transition in the abundance, complexity and sequence content of these sporadic structural variants during crisis. By integrating parallel sequencing datasets, we provide a multifaceted characterisation of replicative crisis in unprecedented detail. Our findings demonstrate that telomere dysfunction and transcription-driven chromatin reorganisation combine to connect replication stress to telomere fusions, eccDNA emergence and genome instability, generating dynamic biomarkers of cellular stress relevant to cancer progression.