Whole genome doubling drives oncogenic loss of chromatin segregation [ChIP-seq]

Whole genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies. However, the 3D organization of the chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here, we show that in p53 deficient cells WGD induces loss of chromatin segregation (LCS), characterized by reduced segregation between short and long chromosomes, A and B sub-compartments, and adjacent chromatin domains. LCS is driven by downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primed genomic regions for sub-compartment repositioning in WGD cells, which resulted in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Importantly, sub-compartment repositioning events were largely independent of chromosomal alterations, indicating that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, suggesting that chromatin evolution is a hallmark of WGD-driven cancer. Overall design: To assess the epigenetic landscape of pre- and post-WGD cells, in vitro and in vivo, chromatin immunoprecipitation sequencing was performed in RPE TP53-/- and CP-A TP53-/- in control and WGD cells, as well as in 20w pWGD tumours derived from RPE TP53-/- cells. WGD samples were assessed for H3K9me3 and CTCF, whereas control and post-WGD in vivo samples were assessed for CTCF, H3K9me3, H3K27ac, H3K27me3, H3K4me3. All samples were performed in one replicate. Mouse spike-in chromatin was included in a fraction of samples, as indicated.