Fig. 2: Genome-wide RNA Polymerase profiling by CUT&Tag in Mtb.

A RNA Pol-CUT&Tag high confidence peak annotation in standard growth condition (STD, blue bars) and upon oxidative stress (OX, orange bars). “Feature” stands for “gene”; “Include feature” indicates the peaks that extend over the whole gene coding sequence. B RNA Pol-CUT&Tag mean signal distribution at high confidence peaks. Average plots (top panel) and density heatmaps (bottom panel) of CUT&Tag reads in standard growth (STD, blue) and oxidative stress (OX, orange) conditions referring to peaks center, within ± 3 kb distance. C Visualization tracks of RNA Pol-CUT&Tag profiles, referred to known RNA Pol binding sites. Gene annotation is reported at the bottom of each track. D Expression levels of Mtb genes presenting (+) or not presenting (−) RNA Pol-CUT&Tag peaks in standard growth (left panel) and in oxidative stress conditions (right panel). Statistical differences were analyzed using unpaired t-test with two tails (STD: n (+) = 866, n (−) = 2649, p-value < 0.0001 (****); OX: n (+) = 740, n (−) = 2637, p-value < 0.0001 (****)); Mean values are reported as horizontal black lines. E Volcano plot illustrating differentially expressed genes upon oxidative treatment. Significant up/downregulated genes were identified using Deseq2 with p-value = 0.05 and Log2FC = 1. Dark brown dots indicate RNA polymerase-retrieved genes identified in oxidative stress conditions. Genes reported to be implicated in the response to oxidative stress are highlighted. Source data are provided as a Source Data file and supporting data 3.