Adaptive replication origin activation alters chromatin dynamics and stability in cancer cells

Abstract

Genome duplication, critical for cell survival and identity, requires precise origin activation to ensure accurate DNA replication and chromatin structure maintenance. In colorectal cancer cells, prolonged replication stress does not hinder cell proliferation, although the mechanisms driving cancer cell adaptability remain largely unclear. Here, we demonstrate that upon recovery, cancer cells are able to activate new replication origins in distinct domains, causing persistent changes in chromatin accessibility, nuclear morphology, and replication timing, ultimately promoting chromatin instability. Chromatin accessibility, particularly in promoter regions, increased following replication stress in a subset of cells, correlating with altered gene expression and nuclear expansion. Additionally, some genes with enhanced promoter accessibility displayed sustained expression changes, further suggesting a transcriptional shift linked to stress adaptation. Our findings reveal that colorectal cancer cells recover from severe replication stress through new origin activation, a mechanism that not only maintains cell proliferation under stress but may also accelerate tumour heterogeneity. This research underscores replication origin activation as a potential therapeutic target in combating cancer cell resilience. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/626323v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@18c8779org.highwire.dtl.DTLVardef@11249f1org.highwire.dtl.DTLVardef@1b46ecaorg.highwire.dtl.DTLVardef@d5a31c_HPS_FORMAT_FIGEXP M_FIG C_FIG MAIN HIGHLIGHTSO_LIColorectal cancer cells under severe replication stress activate new replication origins upon recovery. C_LIO_LIThe firing of new origins in distinct replication domains results in long-lasting changes in chromatin accessibility, especially in promoter regions, and is associated with alterations in nuclear morphology and replication timing. C_LIO_LIIncreased chromatin accessibility in certain promoter regions correlates with prolonged gene expression changes. C_LIO_LIThe capacity of CRC cells to recover from severe replication stress fosters chromatin instability and tumour heterogeneity. C_LI