DNA replication timing and three-dimensional (3D) genome organisation are associated with distinct epigenome patterns across large domains during differentiation and cancer progression. However, it is unclear if alternations in the epigenome, in particular cancer-associated DNA hypomethylation, can directly promote higher order genome architectural alterations. Here, we use Hi-C and single cell Repli-Seq, in the colorectal cancer DNMT1 and DNMT3B DNA methyltransferases double knockout model, to determine the impact of DNA hypomethylation on replication timing and 3D genome organisation. First, we find that the hypomethylated cells show a striking loss of replication timing precision with gain of intra-population replication timing heterogeneity and loss of 3D genome compartmentalisation. Second, hypomethylated regions that undergo a large change in replication timing also show loss of allelic replication timing, including at cancer-related genes. Finally, we observe the striking formation of ectopic H3K4me3-H3K9me3 domains across hypomethylated regions where late replication is maintained, which we propose serve to prevent aberrant transcription and loss of genome organisation after DNA demethylation. Together, our results highlight a previously underappreciated role for DNA methylation in the maintenance of 3D genome architecture.

中文翻译：

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需要DNA甲基化来维持DNA复制定时精度和3D基因组完整性

DNA复制时机和三维（3D）基因组组织与分化和癌症进展过程中跨大域的独特表观基因组模式相关。然而，尚不清楚表观基因组中的改变，特别是与癌症相关的DNA低甲基化，是否可以直接促进更高阶的基因组结构改变。在这里，我们在结直肠癌DNMT1和DNMT3B DNA甲基转移酶双敲除模型中使用Hi-C和单细胞Repli-Seq，来确定DNA低甲基化对复制时机和3D基因组组织的影响。首先，我们发现低甲基化的细胞显示出惊人的复制时机精度损失，其中种群内复制时机异质性增加，而3D基因组区室化的损失。第二，复制时机发生较大变化的低甲基化区域也显示等位基因复制时机的损失，包括与癌症相关的基因。最后，我们观察到跨低甲基化区域中异位H3K4me3-H3K9me3结构域的惊人形成，在该区域中，后期复制得以维持，这建议用于防止DNA脱甲基后的异常转录和基因组组织的丢失。总之，我们的结果突出了DNA甲基化在维持3D基因组结构方面的作用，这一作用先前未被重视。我们提出的这种方法可以防止DNA脱甲基后异常转录和基因组组织的丢失。总之，我们的结果突出了DNA甲基化在维持3D基因组结构方面的作用，这一作用先前未被重视。我们提出的这种方法可防止DNA去甲基化后异常转录和基因组组织丢失。总之，我们的结果突出了DNA甲基化在维持3D基因组结构方面的作用，这一作用先前未被重视。