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. 2021 Apr 20;12:2344. doi: 10.1038/s41467-021-22552-y

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© The Author(s) 2021

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. 6 — a PARIS2 validates predicted structures (black arcs) and reveals new alternative conformations (colored arcs) in the 699 nt 5′UTR of the US47 strain of EV-D68. 5′CL cloverleaf structure, IRES internal ribosome entry site, including domains II–VI, a1–a5 five alternative conformations. Numbers in parentheses are the counts of gapped alignments in each DG. b Long-range structures connecting the 5′UTR to the rest of the genome in two EV-D68 strains. All DGs have cov ≥ 0.01 for these two samples. The two stars indicate the right-side anchors for the strongest long-range strucgtures in the two strains, near the CRE and the region near the stop codon at the end of peptide 3D (3Dstop). c Long-range structures in the 5′UTR are primarily anchored in three linker regions L1–L3 (e.g., L1 is after domain I). d Diagram showing the three strongest long-range structures L1-CRE (connecting L1 and near CRE, in US47), L2L3-start (start codon, in US47), and L1L2-3Dstop (in VR1197). e–g DGs supporting the three long-range structures. In L1-CRE (e), the first ~5000 nt of the genome is shown. In the L2L3-start (f), the first ~800 nt of the genome is shown. In L1L2-3Dstop (g), the entire genome is shown. h Quantifying the strength of DGs for the three structures in all conditions. H HeLa cells, S SH-SY5Y cells, U US47, V VR1197, A AG, G GA. i Stability of the three structures, measured in minimal free energy (MFE), in the two strains.