Genomic and Epigenomic Footprints of Centromeres at Telomeres Define ALT Cancers
Alternative Lengthening of Telomeres (ALT) is a specialized telomere extension mechanism associated with 5-10% of all cancers. Though linked with epigenetic dysregulation and genome instability, specific genomic and epigenetic rearrangements generated upon ALT activation have not been identified. Here, we report the direct insertion of centromeric alpha-satellite repeats and CENP-B boxes adjacent to telomeric repeat sequences at chromosome ends as a defining genomic feature of ALT cancers. Similar insertions were identified among a cohort of ALT pediatric neuroblastomas, indicative of a recurrent pathological link for this unique alteration. Directed methylation with long-read sequencing (DiMeLo-seq) revealed discrete footprints of CENP-A chromatin assembled at telomeric regions on a subset (2-3) of chromosomes. Mechanistically, we show that modeling ALT activation by ATRX disruption is sufficient for acquiring centromeric chromatin signatures, precisely at sites of acute DNA hypomethylation. Furthermore, interfering with newly synthesized CENP-A deposition by depleting HJURP abrogates ALT processes, compromises telomere integrity, and leads to the stimulation of telomeric mitotic DNA synthesis (MiDAS) coordinated by RAD52-SLX4-Pol-delta and Pol-nu We propose that while originally generated by illegitimate recombination between centromeric and telomeric sequences, these centromeric signatures became integral to maintain telomere integrity in the unique context of ALT cancer cells.