Figure 2

Coverage profile of selected regions determined using RNA-seq. Coverage refers to parental (DB110) strain at high (28 MPa, first lane from top) and low pressure (0.1 MPa second lane from top) and for the mutant (TW30) strain in the same conditions (third and fourth lanes). (a) toxR gene, the region having zero coverage in TW30 strain is due to the deletion on the gene. (b) Coverage determined using RNA-seq on the chr. 2 region containing the gene coding for the OmpC porin (an example of a differentially expressed gene). Note the very different coverage between the parental strain grown at high (first lane from top) and low pressure (second lane). The gene does not show difference in coverage comparing TW30 strain grown at high and low pressure (third and fourth lane). In the left part of the picture there is a feature representing a sRNA (PBPRB1638a) overlapped to the 3^′-end of a protein-coding gene. A curious point is that, an analysis of the E. coli genome upstream of the gene coding the OmpC porin, revealed a sRNA in the same position. 5^′ (white boxes) and 3^′-UTRs (yellow boxes) of the genes are highlighted. (c-d) The chr. 2 region containing the CRISP elements gene cluster. In (c) we report the coverage determined by the reads uniquely mapped on the genome (maximum coverage is 25X), while in (d) the coverage is referred both to unique and repeated reads (maximum coverage is 50X). The blue rectangles are the Rfam predictions that clearly overlap with the RNA-seq coverage profile.