DNA replication timing is associated with epigenomic changes during human differentiation and between normal and cancer. A largely unaddressed question to date is whether alterations of the epigenome can ‘drive’ changes in DNA replication timing? DNA methylation in particular has been related to replication timing. Indeed, methylation imprinting appears to delineate which allele replicates early or late during S-phase (e.g. IGF2 and SNRPN, Kitsberg et al. 1993 Nature), and 5’-azacytidine treatment of cancer patient lymphoblasts induces replication timing changes in key cancer genes such as RB1 (Dotan et al. 2008 BMC Cancer).
Here, to investigate whether alterations in DNA methylation can cause a change in DNA replication timing genome-wide, I profiled replication timing (Repli-Seq) in the colorectal cancer cell line HCT116, and the corresponding DNA methyltransferases DNMT1 and DNMT3B double knockout cell line (DKO1). Despite the global DNA hypomethylation in DKO1 cells, the overall replication timing landscape remained largely unperturbed. However, DKO1 showed a loss of precision of replication timing, indicating a loss of synchronicity of replication origins.
Further, regions that showed a large change in replication timing were related to loss of allelic replication timing and shrinking of late-replicating partially methylated domains (PMDs), whereby PMD boundaries became earlier replicating in DKO1. Interestingly, late-replicating PMDs that were maintained between HCT116 and DKO1 coincided with the formation of a non-canonical bivalent domain, H3K9me3/H3K4me3. The H3K9me3/H3K4me3 domains also appeared to protect against aberrant gene activation in DKO1, suggesting that the formation of these bivalent domains may be a ‘rescue’ mechanism to maintain genome function in response to DNA methylation loss.
In summary, global DNA methylation loss reduces the precision of replication timing and induces earlier replication timing at PMD boundaries. However, the DKO1 cells may have evolved to protect against large changes in replication timing through changes in the chromatin landscape.