Abundant contribution of short tandem repeats to gene expression variation in humans
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Abstract
The contribution of repetitive elements to quantitative human traits is largely unknown. Here we report a genome-wide survey of the contribution of short tandem repeats (STRs), which constitute one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from that of linked SNPs and indels and found that eSTRs contribute 10-15% of the cis heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, colocalize with regulatory elements and may modulate certain histone modifications. By analyzing known genome-wide association study (GWAS) signals and searching for new associations in 1,685 whole genomes from deeply phenotyped individuals, we found that eSTRs are enriched in various clinically relevant conditions. These results highlight the contribution of STRs to the genetic architecture of quantitative human traits.
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A recent study demonstrated that the causal variants underlying the strongest common variant association in schizophrenia include duplications of Complement factor 4A.
“a recent study has demonstrated that the causal variants underlying the strongest common variant association in SCZ include duplications of Complement factor 4A 35.”
From Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects (2017) · cites this paper as [35]
Healthy individuals have tens of thousands of relatively short STR tracts distributed throughout their genomes.
“Healthy individuals have tens of thousands of relatively short STR tracts distributed throughout their genomes (Gymrek and Erlich, 2013; Gymrek et al., 2016; Willems et al., 2017).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Gymrek et al., 2016
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Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects
Marshall, C. R., Howrigan, D. P., Merico, D., Thiruvahindrapuram, B., Wu, W., Greer, D. S., Antaki, D., Shetty, A., Holmans, P. A., Pinto, D., et al. (2017) · Nature Genetics · doi:10.1038/ng.3725 · Cited by 1,058 · see citing works
Self-citationAshley, E. A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.86 · Cited by 1,116 · see citing works
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
Tandem repeats mediating genetic plasticity in health and disease
Hannan, A. J. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.115 · Cited by 446 · see citing works
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z. A., Pacis, A., Dumaine, A., Grenier, J.-C., Freiman, A., Sams, A. J., Hebert, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.025 · Cited by 512 · see citing works
Roles of transposable elements in the regulation of mammalian transcription
Fueyo, R., Judd, J., Feschotte, C., & Wysocka, J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00457-y · Cited by 451 · see citing works
The impact of structural variation on human gene expression
GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3834 · Cited by 495 · see citing works
Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.027 · Cited by 480 · see citing works
The sequences of 150,119 genomes in the UK Biobank
Halldorsson, B. V., Eggertsson, H. P., Moore, K. H. S., Hauswedell, H., Eiriksson, O., Ulfarsson, M. O., Palsson, G., Hardarson, M. T., Oddsson, A., Jensson, B. O., et al. (2022) · Nature · doi:10.1038/s41586-022-04965-x · Cited by 448 · see citing works
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions
Dolzhenko, E., Deshpande, V., Schlesinger, F., Krusche, P., Petrovski, R., Chen, S., Emig-Agius, D., Gross, A., Narzisi, G., Bowman, B., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz431 · Cited by 394 · see citing works
Genome-wide profiling of heritable and de novo STR variations
Willems, T., Zielinski, D., Yuan, J., Gordon, A., Gymrek, M., & Erlich, Y. (2017) · Nature Methods · doi:10.1038/nmeth.4267 · Cited by 329 · see citing works
Rafehi, H., Szmulewicz, D. J., Bennett, M. F., Sobreira, N. L. M., Pope, K., Smith, K. R., Gillies, G., Diakumis, P., Dolzhenko, E., Eberle, M. A., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.05.016 · Cited by 262 · see citing works
Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
Sun, J. H., Zhou, L., Emerson, D. J., Phyo, S. A., Titus, K. R., Gong, W., Gilgenast, T. G., Beagan, J. A., Davidson, B. L., Tassone, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.005 · Cited by 249 · see citing works
“Healthy individuals have tens of thousands of relatively short STR tracts distributed throughout their genomes (Gymrek and Erlich, 2013; Gymrek et al., 2016; Willems et al., 2017).”
BackgroundWendt, F. R., Pathak, G. A., & Polimanti, R. (2022) · Nature Communications · doi:10.1038/s41467-022-35423-x · Cited by 12 · see citing works
- Authors
- Gymrek, M., Willems, T., Guilmatre, A., Zeng, H., Markus, B., Georgiev, S., Daly, M. J., Price, A. L., Pritchard, J. K., Sharp, A. J., & Erlich, Y.
- Affiliations
- Broad Institute (US)
- New York Genome Center (US)
- Hôpital Robert-Debré (FR)
- MIT Computer Science and Artificial Intelligence Laboratory (US)
- Whitehead Institute for Biomedical Research (US)
- Stanford University (US)
- Howard Hughes Medical Institute (US)
- Icahn School of Medicine at Mount Sinai (US)
- Corresponding author
- Erlich, Yaniv
- ORCID
- Venue
- Nature Genetics
- Published
- 2015-12-07
- Volume
- 48
- Issue
- 1
- Pages
- 22-29
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4909355
- OpenAlex
- W2227356030
- Cited by
- 410
- References
- 85
- Citations by year
- 2026: 25 · 2025: 37 · 2024: 53 · 2023: 38 · 2022: 54 · 2021: 43 · 2020: 28 · 2019: 33 · 2018: 40 · 2017: 38 · 2016: 21
- FWCI
- 22.55
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Burroughs Wellcome Fund
- National Institutes of Health (1r01da033660-01, 1s10od018522-01)
- National Institute of Mental Health (MH097018, R01MH084703, R01MH097018)
- National Institute on Drug Abuse (DA033660, R01-DA033660)
- National Human Genome Research Institute (U01HG007037, HG006696, R01HG006399, R01HG006696)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- microsatellite markers, expression quantitative trait loci, gene expression variation, repetitive elements, common genetic variants, histone modifications, regulatory elements
- MeSH terms
- Crohn Disease, Histones, Humans, Models, Genetic, Regulatory Sequences, Nucleic Acid, Twins, Genetic Variation, Gene Expression, Genome, Human, Microsatellite Repeats, Polymorphism, Single Nucleotide, Quantitative Trait Loci, INDEL Mutation, Genome-Wide Association Study
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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