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. 2022 Oct 5;611(7934):105–114. doi: 10.1038/s41586-022-05288-7

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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. 3 — a, Methylation frequency of NUMTs in 39 individuals. Colours correspond to the number of long reads that are not affected by the sequencing depth. b, Methylation status of a concatenated NUMT from a father–proband pair. From the outside: (1) methylation frequency of the concatenated NUMT in the father; (2) the ratio of methylation frequency between the NUMT and the non-methylated mtDNA sequence in the father; (3) methylation frequency of the concatenated NUMT in the proband; (4) the ratio of methylation frequency between the NUMT and the non-methylated mtDNA sequence in the proband. Green dots show methylated sites. This analysis includes only reads that were definitively nuclear in origin. The colour corresponds to the methylation frequency. c, Methylation profile for five families (fam1–fam5) with concatenated NUMTs (Supplementary Table 7). From the outside: father, mother, sibling (when available) and proband. Individuals harbouring concatenated NUMTs had higher methylation levels than the individuals without concatenated NUMTs. The colour corresponds to the methylation frequency. d, Three de novo NUMTs from two trios. e, The frequency of mtDNA insertion from germline and tumour-specific NUMTs. From the outside: (1) frequencies of breakpoints from germline NUMTs; (2) frequencies of mtDNA fragments from germline NUMTs; (3) frequencies of breakpoints from tumour-specific NUMTs; (4) frequencies of mtDNA fragments from tumour-specific NUMTs; (5) frequencies of mtDNA sequences expected by chance; (6) mtDNA regions. f, Distribution of breakpoints on mitochondrial genes with germline NUMTs, tumour-specific NUMTs and mitochondrial deletions (window size = 100 bp). The triangle size indicates the frequency of NUMTs within each window. g, P values for enrichment analysis of different genome regions (Supplementary Figs. 1–3 and Methods). Microsat, microsatellite; rmsk-DNA, repetitive DNA; snRNA, small nuclear RNA; srpRNA, signal recognition particle RNA; superdups, superduplications. h, The distance of NUMT locations from the TSS. i, The proportion of NUMTs within genes with high and low pLI scores grouped by NUMT frequency (left) and grouped by NUMT size (right).