Fig. 3

Identification and verification of 5′ UTR small RNAs. a Genes with small RNAs encoded in their 5′ UTRs are functionally categorized using the following abbreviations: CD, cell division; CE, cell envelope; CM, cell motility; MT, metabolism; PD, protein degradation and folding; SR, stress response; TL, translation; TR, transcription; RM; RNA metabolism; DM, DNA metabolism; VM, vitamin metabolism and U, unknown. b A 5′ UTR small RNA (SR0902) was confirmed via Northern blot analyses for bba57. The deep sequencing results are displayed in a coverage map as described in the Fig. 2 legend, except the yellow box indicates the region called as a small 5′ UTR RNA by our peak finder. c Northern blot analyses of total RNA fractionated on a denaturing polyacrylamide gel, blotted to a nylon membrane, and hybridized with oligonucleotides. The predicted transcripts are denoted and marked with the appropriate band (* for sRNA and ^ for mRNA) in the Northern blot. Two independent experiments were performed and representative data are shown