ArticleScientific reports2019
An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.Journal of clinical microbiology · 2022Pooled it
- Article
- The role of cytochrome bcNature communications · 2025Article
- Integrating genomic, transcriptomic, and phenotypic information to explore drug resistance in Mycobacterium tuberculosis sub-lineage 4.2.2.2.Journal of applied microbiology · 2025Article
- Th9 cells provide protective TB immunity.Frontiers in immunology · 2025Article
- Crosstalk between 6-methyladenine and 4-methylcytosine iniScience · 2024Article
- Transcriptome analysis and molecular characterization of novel small RNAs in Mycobacterium tuberculosis Lineage 1.World journal of microbiology & biotechnology · 2024Article
- Article
- Functional genetic variation inFrontiers in microbiology · 2023Article
- Article
- Differences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp.Microbiology spectrum · 2022Article
- Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains.Nature communications · 2022Article
- Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data.Briefings in bioinformatics · 2022Article
- Contribution and Future of High-Throughput Transcriptomics in Battling Tuberculosis.Frontiers in microbiology · 2022Review
- DNA Methyltransferase HsdM Induce Drug Resistance onAntibiotics (Basel, Switzerland) · 2021Article
- Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged withEpigenetics · 2021Article
- Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches.Frontiers in immunology · 2021Review
- MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis.Frontiers in bioinformatics · 2021Article
- Article
- Genetic Diversity inAnnual review of genetics · 2020Review
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10 authors.
Funding
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.
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