School of Natural and Sciences, Massey University, Auckland 0745, New Zealand.
G3 (Bethesda). 2023 Feb 9;13(2). doi: 10.1093/g3journal/jkac310.
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
细菌中的 DNA 甲基化通常作为一种简单的免疫系统，允许识别来自噬菌体或自私遗传元件等外源来源的 DNA。然而，DNA 甲基化也以可遗传的方式（即表观遗传）影响其他细胞表型。虽然有几个例子表明，在高度局部化的情况下，甲基化以表观遗传的方式影响转录，但甲基化在多大程度上以更普遍的表观遗传功能在更大的基因组范围内发挥作用还没有得到很好的确定。为了解决这个问题，我们在这里使用牛津纳米孔测序技术在三种自然分离的大肠杆菌中对 DNA 修饰标记进行了分析。我们首先确定了每种菌株中甲基转移酶靶向的 DNA 序列基序。然后，我们在不同的生长条件下，在整个基因组中定量测定这些基序的甲基化频率。我们发现基因组特定区域的基序始终表现出高或低水平的甲基化。此外，我们还表明，在不同的生长条件下，甲基化区域存在可重复和一致的差异。这表明，在生长过程中，大肠杆菌会短暂地分化为依赖于生长状态的不同甲基化状态，这增加了一种可能性，即仅通过测量 DNA 甲基化就可以推断细菌的生长状态，而无需转录组或蛋白质组等其他信息。这些结果表明，使用牛津纳米孔测序作为一种经济的方法来推断 DNA 甲基化状态是有用的。它们还提供了关于细菌生长过程中甲基化动态的新见解，并提供了分化细胞状态的证据，这是多细胞生物中细胞类型分化所观察到的短暂类似物。
