Table 2.
The Hha/YdgT-dependent and -independent genes up-regulated in the hns/stpA mutant, and their distribution in and around the ‘intergenic’ and ‘coding’ H-NS-binding regions
| Genes up-regulated in hns/stpA mutanta | Genes with intergenic H-NS binding | Genes with coding H-NS binding |
Genes without H-NS-binding regionsb | |
|---|---|---|---|---|
| Hha/YdgT-independent (436 genes) | 136 (31%)c | 243 (55%) | 57 (13%) | |
| Single | Multiple | |||
| 25 (6%) | 218 (50%) | |||
| Hha/YdgT-dependent (122 genes) | 11 (9%)d | 108 (88%) | 3 (2%) | |
| Single | Multiple | |||
| 12 (10%) | 96 (79%) | |||
aTwenty-five genes that were found to be up-regulated in the hns/stpA mutant cells (as detected by transcriptome analysis using the E. coli genome 2.0 array) were not annotated in the genome sequence of E. coli K-12 strain W3110, which was used to design the custom tiling chip for ChIP-chip analysis. We evaluated the correlation of transcriptome alteration and H-NS binding profiles according to the W3110 annotation, and analysed the locations of the 436 genes up-regulated only in the hns/stpA mutant and the 122 genes up-regulated in both the hns/stpA and hha/ydgT mutants. Genes located in or around the H-NS-binding regions were classified as ‘coding’ or ‘intergenic’, respectively.
bSum of the genes that were not located in or around the H-NS-binding regions but showed up-regulation in the hns/stpA mutant alone or in both the hns/stpA and hha/ydgT mutants.
cNumber and percent with respect to the 436 genes up-regulated only in the hns/stpA mutant.
dNumber and percent with respect to the 122 genes up-regulated in both the hns/stpA and hha/ydgT mutants.