DNA methyltransferase 1 (DNMT1) is an important component of the epigenetic machinery and is responsible for copying DNA methylation patterns during cell division. Coordination of DNA methylation and DNA replication is critical for maintaining epigenetic programming. Knockdown of DNMT1 leads to inhibition of DNA replication, but the mechanism has been unclear. Here we show that depletion of DNMT1 with either antisense or small interfering RNA (siRNA) specific to DNMT1 activates a cascade of genotoxic stress checkpoint proteins, resulting in phosphorylation of checkpoint kinases 1 and 2 (Chk1 and -2), ␥H2AX focus formation, and cell division control protein 25a (CDC25a) degradation, in an ataxia telangiectasia mutatedRad3-related (ATR)-dependent manner. siRNA knockdown of ATR blocks the response to DNMT1 depletion; DNA synthesis continues in the absence of DNMT1, resulting in global hypomethylation. Similarly, the response to DNMT1 knockdown is significantly attenuated in human mutant ATR fibroblast cells from a Seckel syndrome patient. This response is sensitive to DNMT1 depletion, independent of the catalytic domain of DNMT1, as indicated by abolition of the response with ectopic expression of either DNMT1 or DNMT1 with the catalytic domain deleted. There is no response to short-term treatment with 5-aza-deoxycytidine (5-azaCdR), which causes demethylation by trapping DNMT1 in 5-aza-CdR-containing DNA but does not cause disappearance of DNMT1 from the nucleus. Our data are consistent with the hypothesis that removal of DNMT1 from replication forks is the trigger for this response.Maintenance of the epigenome is crucial for normal gene expression and preservation of cell identity. The "epigenome" is the set of heritable properties encoded by elements other than DNA base sequence. The epigenome includes chromatin, which is fashioned by remodeling complexes and modification enzymes as well as a pattern of covalent modification of DNA by methylation. During cell division replication of both the genetic and epigenetic, information is faithfully conserved. Due to a preference for hemimethylated DNA, DNA methyltransferase 1 (DNMT1) is believed to be responsible for copying the DNA methylation pattern within the mother cell and maintaining the pattern of genomic methylation within the daughter cell (38). Several lines of evidence suggest a role for DNMT1 in cellular transformation (2,22,23,37,44): indeed, DNMT1 is upregulated in multiple human cancers (17, 33), and some colorectal cancers have been observed to bear mutations in DNMT1 (19). DNMT1 has therefore been proposed as a target for anticancer therapy (39). Indeed, preclinical studies using antisense to DNMT1 have already shown reversion of tumor growth both in vitro (9) and in vivo (29). Taken together, these data suggest an important role for DNMT1 in both maintaining the epigenome and controlling cell cycle.A loss of DNMT1 during replication would result in a loss of epigenetic information. It has therefore been proposed that cells have developed multiple ways...