Fig. 3
Cutoff re-evaluation (RRS) and antisense TSS. A Cutoff re-evaluation. The relative change (RC) of the TSS composition in unexpected genomic positions compared to all genome positions is shown depending on the relative read score (RRS) cutoff (RCRRS = TSSunexpected_RRS/TSSgenome_RRS). TSSgenome includes all possible expected and unexpected TSS signals (TSSgenome = TSSexpected + TSSunexpected). The above-mentioned relative change is shown for three possibilities of TSSexpected: TSS in intragenic region (e.g., degradation signals) and in the 5’ UTR (gTSS, upper panel); TSS only in intragenic regions (middle panel); TSS only in the 5’ UTR (lower panel). A cubic square smooth function (blue line) is placed on the data (dots). A relative read score of 1.5 is indicated with black vertical lines in each panel. The insets exemplary illustrate the analyzed TSS in each case. Black vertical bars, expected TSS in gene regions; red vertical bars, TSS in unusual location, unexpected TSS; dark blue horizontal arrows, coding region of a gene; light blue horizontal bars, 100 bp long 5’ UTR of a gene. B Genomic localization and Cappable-seq sequencing reads for the cis-acting regulatory RNAs symR, sibA, sibC, and sibE. Transcription start sites are indicated with dashed arrows and lines for the annotated gene (black) and the antisense RNA (red). Reads of replicate I in exponential phase, LB, are shown