Figure 3

Comparing conserved intergenic sRNAs: structure and expression analyses. (A) Venn diagram illustrating sRNA conservation in S. coelicolor, S. avermitilis and S. venezuelae. (B-D) Structure, expression profiles and northern blot analyses of conserved sRNAs: (B) scr0999, scr2634, sar5413 and svr2416; (C) scr5583, sar2652 and svr5279; (D) scr1434, sar6912 and svr1031. For (B-D): predicted conserved secondary structures for each sRNA are shown to the far left. Non-standard bases are indicated as follows: M (A or C), R (A or G), W (A or U), S (G or C), Y (C or U), K (G or U), D (not C). Insertions are denoted in lower case. For the expression profiles: positive strand coverage is shown above the gene annotation in red (long transcript library) and orange (sRNA-enriched library); negative strand profiles (below annotation) are shown in blue (long transcript library) and green (sRNA-enriched library). Northern blots showing the temporal expression of each sRNA (time of RNA extraction is indicated in hours) are shown below each coverage graph. For each blot, 5S rRNA was also probed as a control for RNA integrity and abundance.