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. 2022 Mar 11;13:1279. doi: 10.1038/s41467-022-28977-3

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© The Author(s) 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. 2 — A Secondary structure of BinJV 3’UTR generated by SHAPE. SL – stem-loop, DB – dumbbell, RCS3 – reverse conserved sequence 3, CS3 – conserved sequence 3, PK – pseudoknot. B Secondary structures of BinJV stem-loops. C Structure-based sequence alignment between BinJV and MBF xrRNAs. D XRN1 resistance assay with WT and mutated BinJV 3’UTRs. Mutations PK1’ (GAGAG- > CUCUC), PK2’ (UGGUUG- > ACCAAC), nPK1’ (UAGCG- > AUCGC) and nPK2’ (GCGUC- > CGCAG) were introduced into the terminal loop regions of the corresponding stem-loops. The image is representative of four independent experiments that produced similar results. E Densitometry analysis of (D). The values are the means of four independent experiments ± SD. Statistical analysis is two-sided one-way ANOVA. F Consensus structure of dISF xrRNAs built based on the covariance model. Covarying base pairs are highlighted in green (G) Secondary structure of HVV xrRNA generated by SHAPE.