TABLE 1 .
List of regulated noncoding RNAs identified in this study
| Start (bp)a,b | Stop (bp)a,b | Strand | Description | TF regulator(s) | Fold changec |
|---|---|---|---|---|---|
| 34013* | 33811* | − | Antisense to STM14_5565 | HilC | 2.28d |
| 74905 | 74971 | + | DapZ | RtsA | 2.66 |
| 868925 | 868081 | − | Antisense to slrP | RtsA | 1.25 |
| 1343788 | 1343659 | − | STnc520 | SprB | 4.08 |
| 1418433 | 1418523 | + | Overlapping STM14_1613/STM14_1614 | HilC | 1.18 |
| 1603873 | 1604092 | + | MgrR | HilD | 2.12 |
| 1603938 | 1603781 | − | Overlapping STM14_1833 | HilD, RtsA | 3.73, 2.05e |
| 3039507 | 3039347 | − | Antisense to hilA 5′ UTR | HilD | 4.23 |
| 3065151 | 3066061 | + | InvR | HilD, HilC | 1.07, 3.99e |
| 3483808 | 3483985 | + | Within dacB | RtsA | 2.54 |
a
The numbers represent predicted start/stop genome coordinates for a given noncoding RNA (ncRNA). Numbers marked with an asterisk indicate RNAs encoded on the virulence plasmid.
b
In some cases, multiple, overlapping fragments of an ncRNA were identified, or overlapping ncRNAs were identified for multiple TFs. These instances were merged into a single unit.
c
Data represent fold change (log2) in RNA level for cells showing overexpression of the corresponding TF versus cells in which the TF-encoding gene was deleted.
d
Data represent averages of fold change values for three overlapping transfrags.
e
The two values correspond to the 2 TFs, in the order listed in the previous column.