Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a complex disease, with a spectrum of outcomes. Genomic, transcriptomic and methylation studies have revealed differences between Mtb lineages, likely to impact on transmission, virulence and drug resistance. However, so far no studies have integrated sequence-based genomic, transcriptomic and methylation characterisation across a common set of samples, which is critical to understand how DNA sequence and methylation affect RNA expression and, ultimately, Mtb pathogenesis. Here we perform such an integrated analysis across 22 M. tuberculosis clinical isolates, representing ancient (lineage 1) and modern (lineages 2 and 4) strains. The results confirm the presence of lineage-specific differential gene expression, linked to specific SNP-based expression quantitative trait loci: with 10 eQTLs involving SNPs in promoter regions or transcriptional start sites; and 12 involving potential functional impairment of transcriptional regulators. Methylation status was also found to have a role in transcription, with evidence of differential expression in 50 genes across lineage 4 samples. Lack of methylation was associated with three novel variants in mamA, likely to cause loss of function of this enzyme. Overall, our work shows the relationship of DNA sequence and methylation to RNA expression, and differences between ancient and modern lineages. Further studies are needed to verify the functional consequences of the identified mechanisms of gene expression regulation.

由结核分枝杆菌（Mtb）引起的人类结核病（TB）是一种复杂的疾病，具有多种预后。基因组，转录组和甲基化研究表明，Mtb谱系之间存在差异，可能会影响传播，毒力和耐药性。但是，到目前为止，尚无研究在一组普通样品中整合基于序列的基因组，转录组和甲基化表征，这对于了解DNA序列和甲基化如何影响RNA表达以及最终影响Mtb发病机理至关重要。在这里，我们对22 M.结核病进行了这样的综合分析 临床分离株，代表古代（谱系1）和现代（谱系2和4）菌株。结果证实存在谱系特异性差异基因表达，其与基于SNP的表达定量性状位点相关：在启动子区域或转录起始位点有10个涉及SNP的eQTL。和12个涉及转录调节子的潜在功能损伤。还发现甲基化状态在转录中起作用，有证据表明在谱系4个样品的50个基因中有差异表达。甲基化的缺乏与mamA中的三个新变异有关，可能导致此酶功能丧失。总的来说，我们的工作表明了DNA序列和甲基化与RNA表达之间的关系，以及古代和现代血统之间的差异。需要进一步的研究来验证已确定的基因表达调控机制的功能后果。