Figure 3. Distribution of transcriptional activity and RNAP binding sites in the genome of E.coli K12 MG1655.

The genomic map was created with the DNAPlotter [47]. The 1-st and the 2-nd outer circles show the distribution of genes transcribed from different strands. The 3-rd circle shows results of differential expression analysis (RNA-seq data [22]) reflecting the presence of different in size RNAs (plotted as log(N+1), where N is the number of registered sequence reads). The DNAPlotter sliding window was 10 bp, step – 10 bp. Since there was no asymmetry in the transcriptional activity of PIs along the genome, the results obtained for different in length RNAs were shown on one circle divided into 4 sections. A: 44 bases - long sequence reads (productive synthesis); B: samples, which sequences at the 5′-ends match the genome for at lest 14 or 13 bases; C: the same as B for 12 and 11 bases; D: the same as B for 10 and 9 bases. Sequence reads with multiple matching to the genomic DNA were taken into account. The 4th circle shows the distribution of RNAP binding sites (log₂ ratio of hybridization signals, window 300 bp, step 300 bp), revealed by the chip-on-chip technique (experiment B in ref. [34]). Magenta bars mark products transcribed from PIs and hybridization signals within PIs. The central circle shows the local GC-content (window size 300 bp, step 300 bp).