Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle

Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet identified a chromatin modification that correlates with the initiation of DNA replication at particular genomic locations. Here we report that a distinct fraction of replication initiation sites in the human genome are associated with a high frequency of dimethylation of histone H3 lysine K79 (H3K79Me2). H3K79Me2-containing chromatin exhibited the highest genome-wide enrichment for replication initiation events observed for any chromatin modification examined thus far (23.39% of H3K79Me2 peaks were detected in regions adjacent to replication initiation events). The association of H3K79Me2 with replication initiation sites was independent and not synergistic with other chromatin modifications. H3K79 dimethylation exhibited wider distribution on chromatin during S-phase, but only regions with H3K79 methylation in G1 and G2 were enriched in replication initiation events. H3K79 was dimethylated in a region containing a functional replicator (a DNA sequence capable of initiating DNA replication), but the methylation was not evident in a mutant replicator that could not initiate replication. Depletion of DOT1L, the sole enzyme responsible for H3K79 methylation, triggered limited genomic over-replication although most cells could continue to proliferate and replicate DNA in the absence of methylated H3K79. Thus, prevention of H3K79 methylation might affect regulatory processes that modulate the order and timing of DNA replication. These data are consistent with the hypothesis that dimethylated H3K79 associates with some replication origins and marks replicated chromatin during S-phase to prevent re-replication and preserve genomic stability.

哺乳动物的DNA复制以组织特异性模式在特定染色体位点起始，该模式与转录过程协同调控，但此前的相关研究尚未发现可与特定基因组区域内DNA复制起始事件建立相关性的染色质修饰类型。本研究发现，人类基因组中有一类独特的复制起始位点，与组蛋白H3赖氨酸79二甲基化（H3K79Me2）的高频分布存在显著关联。携带H3K79Me2的染色质，其全基因组范围内对复制起始事件的富集程度为目前已检测的所有染色质修饰中最高——23.39%的H3K79Me2峰分布于复制起始事件的邻近区域。H3K79Me2与复制起始位点的关联具有独立性，并不会与其他染色质修饰产生协同效应。H3K79二甲基化在S期的染色质上分布范围更广，但仅在G1期与G2期带有H3K79甲基化的染色质区域，才会富集复制起始事件。H3K79在包含功能性复制起始元件（即可启动DNA复制的DNA序列）的区域中发生了二甲基化；而在无法启动复制的突变型复制起始元件区域内，则未检测到该甲基化修饰。敲除负责催化H3K79甲基化的唯一酶DOT1L后，会触发有限程度的基因组过度复制，尽管多数细胞可在缺乏甲基化H3K79的状态下继续增殖并完成DNA复制。由此可见，阻断H3K79甲基化可能会影响调控DNA复制时序与顺序的生理过程。上述研究结果支持以下假说：二甲基化的H3K79可与部分复制起始位点结合，并在S期标记已完成复制的染色质，从而防止DNA重复复制，维持基因组稳定性。