Supplementary Figures (PDF format)

Figure 1SI. Electropherograms from multiple experiments of TSS mapping for the rpsP gene. All the sequences pointed to the same TSS that is identical to the reported [51], indicating that the DMTSS is a very robust method for mapping initiation events.
Figure 2SI. Unspecific priming of oligonucleotide ybbA into gdhA and sstT genes. A) PCR products obtained with oligonucleotide ybbA, designed for ybbA gene. B) Partial base-pair complementarily of this oligonucleotide with gdhA and sstT regions. Products 1 and 2 correspond to the upstream region of gdhA, while product 3 corresponds to the upstream region of sstT. No product corresponding to gene ybbA, for which the oligonucleotide was designed, was detected.
Figure 3SI. Solving the TSS ambiguity by using a different polynucleotide for the 3’ end labelling. In the case of the ydfH gene, the ambiguity was for only one nucleotide (adenine or guanine. By using a different nucleotide for tailing, for instance thymine instead of adenine, as we did in this case, the ambiguity is solved. This change shows that the guanine nucleotide was indeed the TSS of the ydfH gene under the conditions tested. A) Incorporation of dTTP at the 3’ end of the cDNA. B) Incorporation of dATP at the 3’ end of the cDNA.

Figure 4SI. Gene context of the csrB, tff and sroG small RNA.

Figure 5SI. Location of the TF's sites predicted in the regulatory region of each TU with promoter prediction.

Supplementary Tables (Excel Format)

Table 1SI. Results for prediction of -10 and -35 elements recognized by sigma70 and simga38 with the program PATSER.

Table 2SI. Oligonucleotides utilized for DMTSS.

Table 3SI. Genes with known, predicted, conserved, putative, hypothetical or unknown function.

Table 4SI. Putative binding sites for 55 transcription factors were searched in the regions from -400 to +200 for each TSS with promoter prediction, using the Matriz-Scan program   tfs_scG.txt.
Table 5SI. Transcriptional factors binding sites associated to each TSS. The information in RegulonDB for each of these TFs and their binding sites is shown.
Table 6S1. Predicted Attenuators binding sites for DMTSS.

Additional Images by Experiment