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Transposable element 5mC methylation state of blood cells predicts age and disease.

作者信息

Morandini Francesco, Lu Jinlong Y, Rechsteiner Cheyenne, Shadyab Aladdin H, Casanova Ramon, Snively Beverly M, Seluanov Andrei, Gorbunova Vera

机构信息

Department of Biology, University of Rochester, Rochester, NY, USA.

Herbert Wertheim School of Public Health and Human Longevity Science and Division of Geriatrics, Gerontology, and Palliative Care, Department of Medicine, University of California San Diego, La Jolla, CA, USA.

出版信息

Nat Aging. 2025 Feb;5(2):193-204. doi: 10.1038/s43587-024-00757-2. Epub 2024 Nov 27.


DOI:10.1038/s43587-024-00757-2
PMID:39604704
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11839465/
Abstract

Transposable elements (TEs) are DNA sequences that expand selfishly in the genome, possibly causing severe cellular damage. While normally silenced, TEs have been shown to activate during aging. DNA 5-methylcytosine (5mC) is one of the main epigenetic modifications by which TEs are silenced and has been used to train highly accurate age predictors. Yet, one common criticism of such predictors is that they lack interpretability. In this study, we investigate the changes in TE 5mC methylation that occur during aging in human blood using published methylation array data. We find that evolutionarily young long interspersed nuclear elements 1 (L1s), the only known TEs capable of autonomous transposition in humans, undergo the fastest loss of 5mC methylation, suggesting an active mechanism of de-repression. The same young L1s also showed preferential gain in chromatin accessibility but not expression. The long terminal repeat retrotransposons THE1A and THE1C also showed very rapid 5mC loss. We then show that accurate age predictors can be trained on both 5mC methylation of individual TE copies and average methylation of TE families genome wide. Lastly, we show that while old L1s gradually lose 5mC during the entire lifespan, demethylation of young L1s only happens late in life and is associated with cancer.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/4f2b07398a90/43587_2024_757_Fig11_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/010fa43504cb/43587_2024_757_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/cb2feeb96a10/43587_2024_757_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/c0a644b0afce/43587_2024_757_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/426b9e7893c0/43587_2024_757_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/afb09572f58a/43587_2024_757_Fig5_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/27a8c281e471/43587_2024_757_Fig6_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/339ae355f822/43587_2024_757_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/1e89b48dc9e5/43587_2024_757_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/f2f9e3d18aed/43587_2024_757_Fig9_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/35df8f286e4f/43587_2024_757_Fig10_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/4f2b07398a90/43587_2024_757_Fig11_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/010fa43504cb/43587_2024_757_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/cb2feeb96a10/43587_2024_757_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/c0a644b0afce/43587_2024_757_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/426b9e7893c0/43587_2024_757_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/afb09572f58a/43587_2024_757_Fig5_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/27a8c281e471/43587_2024_757_Fig6_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/339ae355f822/43587_2024_757_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/1e89b48dc9e5/43587_2024_757_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/f2f9e3d18aed/43587_2024_757_Fig9_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/35df8f286e4f/43587_2024_757_Fig10_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b249/11839465/4f2b07398a90/43587_2024_757_Fig11_ESM.jpg

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引用本文的文献

[1]
Unlocking longevity through the comparative biology of aging.

Nat Aging. 2025-8-28

[2]
Transposable element methylation tracks age.

Nat Aging. 2025-2

本文引用的文献

[1]
Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements.

Aging Cell. 2024-10

[2]
PRC2-AgeIndex as a universal biomarker of aging and rejuvenation.

Nat Commun. 2024-7-16

[3]
Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites.

Cell Genom. 2024-2-14

[4]
ATAC-clock: An aging clock based on chromatin accessibility.

Geroscience. 2024-4

[5]
Repetitive DNA sequence detection and its role in the human genome.

Commun Biol. 2023-9-19

[6]
Quantifying the arms race between LINE-1 and KRAB-zinc finger genes through TECookbook.

NAR Genom Bioinform. 2023-9-6

[7]
Downregulation of transposable elements extends lifespan in Caenorhabditis elegans.

Nat Commun. 2023-8-29

[8]
BHLHE22 drives the immunosuppressive bone tumor microenvironment and associated bone metastasis in prostate cancer.

J Immunother Cancer. 2023-3

[9]
Hypermethylation of HIC2 is a potential prognostic biomarker and tumor suppressor of glioma based on bioinformatics analysis and experiments.

CNS Neurosci Ther. 2023-4

[10]
Resurrection of endogenous retroviruses during aging reinforces senescence.

Cell. 2023-1-19

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