Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle
Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle
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DOI：
10.1073/pnas.1319315110
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发表时间：
2013-11-26
影响因子：
11.1
通讯作者：
McAdams, Harley H.
中科院分区：
文献类型：
--
作者：
Kozdon, Jennifer B.;Melfi, Michael D.;McAdams, Harley H.
Caulobacter DNA甲基转移酶（CcrM）是五种主要的细胞周期调节因子之一。当CcrM快速甲基化半甲基化GANTC序列中的腺嘌呤时，它在DNA复制结束时短暂存在。两个主调控基因和两个细胞分裂基因的转录时间由其启动子中GANTC位点的甲基化状态控制。为了探索这种调控机制的全球范围，我们使用单分子实时测序技术确定了细胞周期中五个时间点上整个染色体每个碱基对的甲基化状态。4515个GANTC位点的甲基化状态，优先定位于基因间区域，随着复制分叉的推进，甲基化状态逐渐从完全变为半甲基化。然而，27个GANTC位点在整个细胞周期中保持未甲基化，这表明这些受保护的位点可能参与表观遗传调控功能。通过分析每个细胞周期调控转录起始位点的激活时间，以及GANTC位点在启动子区域的位置和细胞周期中GANTC位点从完全甲基化过渡到半甲基化的时间，可以鉴定出59个基因作为表观遗传调控的候选基因。此外，我们鉴定了两个以前未鉴定的n6 -甲基腺苷基，并表明它们在整个细胞周期中保持恒定的甲基化状态。同源的甲基转移酶被鉴定为这些基序之一以及两个5-甲基胞嘧啶基序之一。
The Caulobacter DNA methyltransferase CcrM is one of five master cell-cycle regulators. CcrM is transiently present near the end of DNA replication when it rapidly methylates the adenine in hemimethylated GANTC sequences. The timing of transcription of two master regulator genes and two cell division genes is controlled by the methylation state of GANTC sites in their promoters. To explore the global extent of this regulatory mechanism, we determined the methylation state of the entire chromosome at every base pair at five time points in the cell cycle using single-molecule, real-time sequencing. The methylation state of 4,515 GANTC sites, preferentially positioned in intergenic regions, changed progressively from full to hemimethylation as the replication forks advanced. However, 27 GANTC sites remained unmethylated throughout the cell cycle, suggesting that these protected sites could participate in epigenetic regulatory functions. An analysis of the time of activation of every cell-cycle regulatory transcription start site, coupled to both the position of a GANTC site in their promoter regions and the time in the cell cycle when the GANTC site transitions from full to hemimethylation, allowed the identification of 59 genes as candidates for epigenetic regulation. In addition, we identified two previously unidentifiedN6-methyladeninemotifs and showed that they maintained a constant methylation state throughout the cell cycle. The cognate methyltransferase was identified for one of these motifs as well as for one of two 5-methylcytosine motifs.