Fig. 3: Effect of resR/mcdR depletion on the whole genome transcriptional profile of Mtb.

a Schematic of the strategy used for whole genome transcriptional profiling of Mtb. Briefly, bacterial cultures of the empty vector control and resR/mcdR(−) (KD) strains were treated with 50 ng/ml ATc for four days, followed by extraction of RNA. After verification of resR/mcdR silencing in the KD by qRT-PCR, samples were processed for RNA sequencing as described in the text. b Volcano plot of differentially expressed genes in resR/mcdR(−). Shown is the distribution of differentially expressed genes via log2 (fold-change) and >1.3 −log p values. Broken vertical lines represent the cutoff of ≥1 log2 fold-change. Genes undergoing downregulation are represented by red dots, and those showing upregulation in resR/mcdR(−) are marked with blue dots. The status of resR/mcdR expression is highlighted by an arrow. Data represent fold change in read counts between resR/mcdR(−) and control strains from three biological replicates. c Functional categorization of differentially expressed genes. Shown is the butterfly chart for the distribution pattern of genes that are perturbed in resR/mcdR(−) according to their function. Different functional categories are defined according to classification by the Mycobrowser database (https://mycobrowser.epfl.ch/genes/). d, e Status of differentially accumulated transcripts. Heat maps represent transcripts showing accumulation (d) or suppression (e) upon resR/mcdR silencing. f Validation of RNAseq data. RNAseq data were verified by qRT-PCR analysis of select genes, using specific primer pairs (Supplementary Data 4). Fold change in expression of the respective transcripts was obtained after normalization with the level of a control gene htpG, which remains constant in both strains. Data represent mean values from multiple (n = 2) biological repeats.