Extended Data Fig. 2: Characterization of Mtb TSSs, TTSs, and asRNAs detected by SEnd-seq.
From: Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome
a, (Top) Schematic showing different categories of TSS based on its location and orientation. (Bottom) Number of gTSSs, iTSSs, and asTSSs in the Mtb genome identified by SEnd-seq. b, Distribution of TSS intensities for the gTSSs (n = 2,584), iTSSs (n = 2,681), and asTSSs (n = 3,608) described in a. The bars indicate mean values with interquartile range. P values were determined using two-tailed Student’s t-test. c, Primary RNA SEnd-seq data track showing an example leaderless TSS in Mtb. d-e, Venn diagram showing the overlap of all TSSs (d) or leaderless TSSs (e) identified by SEnd-seq in this study with those reported by two previous studies7,8. f-g, Motif analysis for the +1 site, −10 element, and −35 element for all Mtb TSSs (f) and leaderless TSSs (g) identified by SEnd-seq. h, SEnd-seq data track showing an example TTS in Mtb. i, Distribution of the termination efficiencies for the TTSs in the Mtb genome identified by SEnd-seq. The lower bound to qualify for a TTS was set to 40%. j, Secondary RNA structure upstream of the example TTS shown in h. (Inset) Motif analysis for the 3′ flanking sequences of the RNA hairpins upstream of all identified Mtb TTSs (n = 121) showing a lack of conserved motif. k, Distribution of the RNA coverage upstream of each TTS identified by SEnd-seq. Only sites with an RNA coverage less than 3,000 are shown here. Note that we cannot detect potential TTSs for very lowly expressed genes due to the read threshold used in our TTS identification criteria (see Methods). l-m, Primary RNA and total RNA SEnd-seq data tracks for two example Mtb genomic regions showing an abundance of antisense RNAs (blue lines). n, Scatter plot showing the anticorrelation between the percentage of asRNAs in each TU (n = 1,930) and the summed coverage of the corresponding coding RNAs. Spearman correlation coefficient is shown. o, SEnd-seq signals for an example Mtb asRNA demonstrating the definition of asRNA length used in this study. p, Distribution of the length of asRNAs identified by SEnd-seq in log-phase Mtb cells.