Abstract
This study assembles DNA adenine methylomes for 93 Mycobacterium tuberculosis 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 ΔhsdM 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.
Highlights
In 2017, tuberculosis (TB) killed 1.6 million people globally, the most of any infectious disease, despite significant TB control efforts and the availability of effective TB drugs (WHO, 2017)
To examine motif sites consistently classified as hypomethylated for previously described causes of hypomethylation (Beaulaurier et al, 2019), we screened against published transcription factor binding sites (TFBSs) affinities (Minch et al, 2015) for interactions with DNA methylation (Supplementary file 5)
Comparative, integrative, and heterogeneity analyses of these methylomes, we identified drivers and sites of variability in DNA adenine methylomes across the Mycobacterium tuberculosis complex (MTBC)
Summary
In 2017, tuberculosis (TB) killed 1.6 million people globally, the most of any infectious disease, despite significant TB control efforts and the availability of effective TB drugs (WHO, 2017). Multidrug-resistant tuberculosis (MDR-TB) threatens control efforts and debilitates patients through a grueling and often ineffective treatment regimen (52% success) (WHO, 2017). Subpopulations of the pathogen consistently persist through chemotherapeutics, eventually developing full antibiotic resistance (Jain et al, 2016). It is unclear how such a genetically static organism adapts so rapidly to drug treatment and varied immune pressures. DNA methylation is a plausible yet scarcely explored alternative mechanism for phenotypic variation in M. tuberculosis. M. tuberculosis encodes three known DNA methyltransferases (MTases), MamA, MamB, and HsdM, which each target a different sequence motif for N6-adenine methylation (Shell et al, 2013; Zhu et al, 2016).
Sign-in/Register to view highlights & summary 
Published Version
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call