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. 2022 Nov 19;13:7115. doi: 10.1038/s41467-022-34810-8

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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. 5 — a All 397 Alu TEMRs by variant type (shape) and Alu density (shading). b TEMRs disproportionately intersect genes (pie chart) affecting introns, exons, and gene-proximal regions that are often enriched with regulatory elements. c Regulatory and coding regions affected by TEMRs. Regulatory annotations were retrieved from ENCODE cCREs, coding regions and TFBS predictions from Ensembl Variant Effect Predictor (VEP). TFBS, transcription factor binding site; cCREs, Candidate Cis-Regulatory Elements; K4m3, DNase-H3K4me3; enhD, distal enhancer-like signature; enhP, proximal enhancer-like signature; prom, promoter-like signature; UTR, untranslated region; ENCODE, the encyclopedia of DNA elements; TEMR, transposable element-mediated rearrangement. d Example of TEMR deleting a stop codon in TRIM65 (bottom).