A B C SCO3042 SCO3043 SCO3044 SCO3045 SCO3046 scr3043 scr3045 SCO3869 SCO3870 scr3870* SCO3973 SCO3974 scr3974 SCO3260 SCO3261 scr3261 SCO5333 SCO5334 scr5334* Nucleic Acids Research, 2008, Vol. 36, No. 22 7249 5′ 3′ 5′ 3′ 288 nt scr3045 5′ 3′ 42 nt scr3974 ~185 nt scr3261 Figure 5. Predicted structure and location of duplicated sRNA sequences within the S. coelicolor chromosome. (A) The sequence encompassing scr3045, SCO3045 and SCO3046 is extremely similar to that of scr3043, SCO3043 and SCO3044, suggesting a possible duplication event in S. coelicolor (other Streptomyces species have only one copy of each gene). Homologous genes are indicated in the same colours (scr3043 and scr3045: black arrows; SCO3043 and SCO3045: dark grey arrows; SCO3044 and SCO3046: white arrows). To the right is the predicted structure of scr3045. (B) The scr3974 sequence is extremely similar to that of a region found between SCO3869 and SCO3870, designated scr3870, although the ﬂanking genes do not bear similarity to each other. To the right is the predicted structure of scr3974. (C) The scr3261 sequence bears striking similarity to a sequence located between SCO5333 and SCO5334, although, again, the ﬂanking sequences are not similar. The scr3261 structure is distinctive due to its extensive internal complementarity. The asterisks in (B) and (C) indicate putative sRNA genes for which transcripts have never been experimentally detected. were probed with unique oligonucleotides ﬂanking this inverted repeat region, and no transcript was ever detected with the scr5334 primers (Supplementary Table S2), while transcripts were observed when using scr3261-speciﬁc pri- mers. As in S. coelicolor, the stem-loop structure of scr3261 is found at multiple sites in S. avermitilis and S. griseus; however, their locations are not syntenous with the scr3261 sequence, suggesting that this sequence might be associated with some type of mobile genetic element. The unusually extensive self-complementarity of the scr3261 transcript would make it a reasonable target for RNase III, which cleaves double stranded RNA. The transcript, however, appears to be stable during growth on rich medium. A possible explanation for this observation would be that scr3261 functions in sequestering a protein and that this in turn protects it from degradation; however, the biological target of scr3261 has yet to be identiﬁed.