Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States.
Trudeau Institute, Saranac Lake, United States.
Elife. 2020 Oct 27;9:e58542. doi: 10.7554/eLife.58542.
This study assembles DNA adenine methylomes for 93 complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling. Second, heterogeneity analysis of partially active methyltransferase alleles revealed that intracellular stochastic methylation generates a mosaic of methylomes within isogenic cultures, which we formalize as 'intercellular mosaic methylation' (IMM). Mutation-driven IMM was nearly ubiquitous in the globally prominent Beijing sublineage. Third, promoter methylation is widespread and associated with differential expression in the transcriptome, suggesting promoter HsdM-methylation directly influences transcription. Finally, comparative and functional analyses identified 351 sites hypervariable across isolates and numerous putative regulatory interactions. This multi-omic integration revealed features of methylomic variability in clinical isolates and provides a rational basis for hypothesizing the functions of DNA adenine methylation in MTBC physiology and adaptive evolution.
本研究为来自七个谱系的 93 株复杂（MTBC）分离株组装了 DNA 腺嘌呤甲基组学，这些分离株与完全注释、完成的、从头组装的基因组配对。综合分析产生了四个关键结果。首先，甲基转移酶等位基因-甲基组学图谱修正了以前被基于参考的变异调用掩盖的甲基转移酶变体效应。其次，部分活性甲基转移酶等位基因的异质性分析表明，细胞内随机甲基化在同基因培养物内产生了甲基组的镶嵌体，我们将其形式化为“细胞间镶嵌甲基化”（IMM）。突变驱动的 IMM 在全球流行的北京亚谱系中几乎无处不在。第三，启动子甲基化广泛存在，并与转录组的差异表达相关，表明启动子 HsdM 甲基化直接影响转录。最后，比较和功能分析确定了 351 个跨越分离株的高变位点和许多假定的调控相互作用。这种多组学整合揭示了临床分离株中甲基组变异性的特征，并为假设 DNA 腺嘌呤甲基化在 MTBC 生理学和适应性进化中的功能提供了合理的依据。
