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. 2022 Jun 22;13:3560. doi: 10.1038/s41467-022-31173-y

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© The Author(s) 2022, corrected publication 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Categories of identified intermolecular RNA interactions. Here, a single interaction can be represented by many hybrids. tRNA-tRNA and rRNA-rRNA chimeras were excluded due to their high sequence similarity, meaning that we could not unambiguously determine if these represented intermolecular or intramolecular interactions. “Total” indicates the total number of unique RNA-RNA interactions identified in each dataset. Colour of each stacked bar denotes the type of interaction represented. b As in a, but only for interactions containing a bona fide sRNA. c Top: distribution of the mRNA fragments in bf sRNA-mRNA interactions around the translational start codon (AUG). Orange line shows data from USA300 and the black line from JKD6009. Bottom: heatmaps showing the read distribution for the mRNA fragments for each individual interaction. Interactions highlighted in green are those that have previously been experimentally verified, and in red are those interactions involving toxins. Interactions coloured in black are other novel interactions identified in this study.