Dynamic genetic regulation of gene expression during cellular differentiation
Open accessAbstract
Variants affect gene expression over time: Genetic variation drives the spectrum of human phenotypes but in some cases has been linked to pathological conditions. Strober et al. set out to explore how genetic diversity regulates gene expression in cell differentiation over time. They examined expression quantitative trait loci (eQTLS)—genetic variants correlated with gene expression—in induced pluripotent stem cell lines from 19 Yoruban individuals at 16 time points during differentiation into cardiomyocytes. They identified hundreds of developmental stage–specific eQTLs. Thus, the impact of genetic variations depends on the developmental context or tissue under observation. Science , this issue p. 1287
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The eQTL framework has clear limitations, including reliance on naturally occurring human genetic variation, linkage disequilibrium, and restriction to cell types and tissues practically obtainable from large numbers of individuals.
“On the other hand, the framework has clear limitations, including its reliance on naturally occurring human genetic variation (most enhancers do not harbour common variants that substantially perturb their activity), linkage disequilibrium [G] (multiple variants in a haplotype block may equivalently explain an association), and restriction to cell types and tissues that can be practically obtained”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [137]
In the paper’s main text (indexed under Abstract; page unavailable), two variants in strong linkage disequilibrium are reported as both associated with SCN5A expression. This illustrates the linkage underlying the cited limitation, but the paper does not say that the variants equivalently explain the association or explicitly identify linkage disequilibrium as a limitation of eQTL analysis. (LLM, conf=0.78)
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References 33 · Cited by 219
- Authors
- Strober, B. J., Elorbany, R., Rhodes, K., Krishnan, N., Tayeb, K., Battle, A., & Gilad, Y.
- Affiliations
- Johns Hopkins University (US)
- University of Chicago (US)
- Corresponding author
- Strober, B. J.
- Elorbany, R.
- Rhodes, K.
- Battle, A.
- Gilad, Y.
- Venue
- Science
- Published
- 2019-06-28
- Volume
- 364
- Issue
- 6447
- Pages
- 1287-1290
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6623972
- OpenAlex
- W2955723825
- Cited by
- 219
- References
- 33
- Citations by year
- 2026: 25 · 2025: 37 · 2024: 47 · 2023: 26 · 2022: 36 · 2021: 26 · 2020: 17 · 2019: 5
- FWCI
- 12.66
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (T32GM007281, 5T32GM007197)
- National Institute of General Medical Sciences (R01GM120167)
- American Heart Association (18PRE34030197)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- expression quantitative trait loci, dynamic gene regulation, cell differentiation, induced pluripotent stem cells, cardiomyocyte differentiation, enhancers, body mass index, cell type-specific gene expression
- MeSH terms
- Cell Differentiation, Cell Line, Gene Expression Regulation, Humans, Sequence Analysis, RNA, Myocytes, Cardiac, Pluripotent Stem Cells, Quantitative Trait Loci
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