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Cited by 28Epigenetics and DNA MethylationGenetic Associations and EpidemiologyForensic and Genetic Research

Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation

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Martin-Trujillo, Alejandro, Garg, Paras, Patel, Nihir, Jadhav, Bharati, Sharp, Andrew J.·2023·Genome Research
DOI 10.1101/gr.277057.122PMC PMC10069470
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Abstract

Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human genome and modify risk of common human traits. To address these questions, we first analyzed two independent data sets comprising PCR-free whole-genome sequencing (WGS) and genome-wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using HipSTR, we identified 11,870 STRs that associated with DNA methylation levels (mSTRs) of 11,774 CpGs (Bonferroni P < 0.001) in our discovery cohort, with 90% successfully replicating in our second cohort. Subsequently, through fine-mapping using CAVIAR we defined 585 of these mSTRs as the likely causal variants underlying the observed associations (fm-mSTRs) and linked a fraction of these to previously reported genome-wide association study signals, providing insights into the mechanisms underlying complex human traits. Furthermore, by integrating gene expression data, we observed that 12.5% of the tested fm-mSTRs also modulate expression levels of nearby genes, reinforcing their regulatory potential. Overall, our findings expand the catalog of functional sequence variants that affect genome regulation, highlighting the importance of incorporating STRs in future genetic association analysis and epigenetics data for the interpretation of trait-associated variants.

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  • A fraction of STRs can act as regulators of genome function by modulating DNA methylation, which may impact molecular mechanisms affecting disease or altering drug-response pathways.

    “This suggests that a fraction of STRs can act as regulators of genome function by modulating DNA methylation, which may impact molecular mechanisms affecting disease or altering drug-response pathways [61].”

    From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [61]

    The Discussion (page not provided) states that a fraction of STRs regulate genome function by modulating DNA methylation in cis and may underlie phenotypic variation and disease. Our copy does not connect this finding to altered drug-response pathways, so that part of the claim is unsupported. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Even samples with a correct STR profile can be impacted or experience methylation drift.

    “Even samples with a correct STR profile can be impacted or experience methylation drift [61],”

    From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [61]

    The Results (Identification of mSTRs with putative regulatory effects; page unavailable) say that factors other than STRs can influence DNA methylation. This supports the general point that an STR genotype does not determine methylation, but the paper does not examine samples with a correct STR authentication profile or show methylation drift over time. (LLM, conf=0.77)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Martin-Trujillo, A., Garg, P., Patel, N., Jadhav, B., & Sharp, A. J.
Affiliations
Icahn School of Medicine at Mount Sinai (US)
Corresponding author
Sharp, Andrew J.
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2022-12-28
Volume
33
Issue
2
Pages
184-196
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.277057.122
PMC
PMC10069470
OpenAlex
W4313279953
Cited by
28
References
4
Citations by year
2026: 8 · 2025: 10 · 2024: 8 · 2023: 2
Type
posted content
Language
en
Open access
Licence
cc-by-nc
Locations
  • Genome Research (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Pediatric Cardiac Genomics Consortium
  • National Heart, Lung, and Blood Institute, National Institutes of Health (NHLBI, NIH), U.S. Department of Health and Human Services (UM1HL128711, UM1HL098162, UM1HL098147, UM1HL098123, UM1HL128761, U01HL131003)
  • NHLBI
  • Michael J. Fox Foundation
  • NIH (R01NS105781)
  • American Heart Association (18POST34080396)
  • NHLBI Biodata Catalyst (5120339)
  • National Institutes of Health (S10OD018522)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
microsatellite markers, DNA methylation, epigenetics, CpG methylation, complex human traits, gene expression regulation, fine mapping, causal variants, genetic diversity
MeSH terms
Genotype, Humans, Genome, Human, Microsatellite Repeats, DNA Methylation, Genome-Wide Association Study

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