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. 2024 Nov 7;25(12):5780–5809. doi: 10.1038/s44319-024-00304-5

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Schematic representation of the strategy used to identify EVD antisense nested insertions within itself from EM-seq discordant paired read mates mapping to EVD-LTR and elsewhere on EVD coding sequence in antisense to the LTR. The table indicates the occurrence and number of read mates found in each sample. Arbitrary threshold of at least two paired read mates by LTR was set to confidentially identify an EVD nested insertion. N: non-occurrence, y: presence of at least one discordant paired read mate, Y: presence of discordant paired read mates and above threshold for confident presence of nested insertion. (B) Scheme of EVD antisense nested insertion structure based on EVD discordant reads in the sample rdr6-EVD F6 #5. Distance between LTRs as well as the length of the target-site duplication (TSD) caused by the insertion are indicated in base-pairs (bp). Colored arrows represent potential EVD transcripts within the locus. Putative sources of small RNAs are depicted below. (C) Schematic representation of methodology used to infer the methylation status of EVD landing sites prior to transposition using the EM-seq data. EVD insertions are represented by red lines. Red boxes indicate regions with new and polymorphic EVD insertions. Blue boxes represent the same region without the EVD insertion. (D) Pie charts of the distribution of insertions within non-methylated, CG-only methylated and non-CG methylated regions within each sample. Inlets represent the classification of non-CG methylated regions into RdDM-, CMT2-dependent or independent of both. Number of insertions in each category is indicated within the chart. (E) Metaplot of the mean shift in DNA methylation following a EVD insertion by genotype and methylation context depending on EVD silencing status. Source data are available online for this figure.