An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome

Paula J Gomez-Gonzalez,Taane G Clark,Paola Florez De Sessions,Nuria Andreu,Jody E Phelan,Philip D Butcher,Susana Campino,Martin L Hibberd,Amelia C Crampin,Judith R Glynn

doi:10.1038/s41598-019-41692-2

Abstract

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.

Highlights

Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a major global public health issue[1]
These effects can be explored through an association analysis of polymorphisms, such as single nucleotide polymorphisms (SNPs), and gene expression levels to determine expression quantitative trait loci. eQTLs are genetic variants that explain variation in gene expression levels, and can be classified as cis or trans depending on the physical distance from the gene they regulate[14]
We present a differential gene expression study correlated with lineage, as well as an eQTL study linked with SNPs and methylated bases at a whole genome scale

Summary

Introduction

Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a major global public health issue[1]. In Mtb, one previous study focusing on lineage 1 and 2 strains, highlighted two types of mechanisms where polymorphisms may change gene expression: through impairment of transcriptional regulators or by affecting the promoter regions[10]. No studies have integrated sequence-based genomic, transcriptomic and methylation characterisation across a common set of samples. This integration is critical to understand how DNA sequence and methylation affect RNA expression and, Mtb pathogenesis. Differential transcription between lineages was found, and genetic variants revealed as potential candidate eQTLs. Methylation status was found to have a potential role in transcription, with evidence of differential gene expression between samples with non-methylated and methylated genes

Methods

Results

Conclusion