Extended Data Fig. 8: Effects of rho knockdown on the Mtb transcriptome.

a, SEnd-seq data track around the Mtb rho gene (Rv1297) from cells with or without ATc-induced sgRNA expression. The sgRNA targeting site is indicated by the purple line. b, Depletion of Rho proteins upon sgRNA expression is verified by western blotting. The RpoB signal serves as a loading control. M indicates the molecular weight marker lane. c, Mtb growth curves with or without ATc-induced rho knockdown. d, Volcano plot showing changes in the expression level of essential Mtb genes (n = 696) upon rho knockdown measured by SEnd-seq. P values were determined using two-tailed Student’s t-test. e, Violin plot showing the distribution of PFs for Mtb coding TUs with or without rho knockdown. TUs that exhibited high expression within a 200-nt window downstream of the TSS in both datasets were selected for analysis (n = 1,679). The solid lines represent the median and the dashed lines represent the quartiles. P value was determined using two-tailed Student’s t-test. f, SEnd-seq data track for an example Mtb genomic region showing an increase in asRNA abundance upon rho knockdown. g, Summed SEnd-seq intensities for Mtb asRNAs aligned at TSSs with or without rho knockdown. Highly expressed asRNAs in the control condition were selected for analysis (n = 1,565). The intensities for each position were normalized to the peak value in the control group. h, Data track for an example Mtb TU showing the RNA-seq results before and after Rho depletion from a previous study¹⁸ and the corresponding total RNA SEnd-seq results from the current study. i, Summed RNA-seq and SEnd-seq intensities for Mtb TUs aligned at TSSs before and after Rho depletion. TUs with a highly expressed upstream zone and a PF < 0.3 in the control condition for wildtype cells were selected for analysis (n = 431). Colored lines represent median values and shaded regions represent s.d.

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