Figure 2.

Determination of the 5′- and 3′-ends of chlamydial ncRNAs using an RNA circularization assay (23). (A) Schematic representation of the RNA circularization procedure, beginning with the removal of the 5′-pyrophosphate using tobacco acid phosphatase (TAP) followed by circularization using T4 RNA ligase. Primers were then designed to amplify the 5′/3′ junction. (B) The 5′- and 3′-ends of the ncRNAs determined in this study. The 5′-end is designated the TSS and the 3′-end and overall size of the ncRNAs is listed. ncRNAs that contained non-templated additions at the 3′-end (primarily poly-A additions of different lengths) are indicated by an asterisk. Promoter predictions were made by examination of the areas immediately upstream of the TSS. All of the predicted promoters were of the σ⁶⁶ (major sigma factor) type and two had an extended −10 sequence.