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A Polymorphism in IRF4 Affects Human Pigmentation through a Tyrosinase-Dependent MITF/TFAP2A Pathway
Open accessAbstract
Sequence polymorphisms linked to human diseases and phenotypes in genome-wide association studies often affect noncoding regions. A SNP within an intron of the gene encoding Interferon Regulatory Factor 4 (IRF4), a transcription factor with no known role in melanocyte biology, is strongly associated with sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color. Here, we demonstrate that this SNP lies within an enhancer of IRF4 transcription in melanocytes. The allele associated with this pigmentation phenotype impairs binding of the TFAP2A transcription factor that, together with the melanocyte master regulator MITF, regulates activity of the enhancer. Assays in zebrafish and mice reveal that IRF4 cooperates with MITF to activate expression of Tyrosinase (TYR), an essential enzyme in melanin synthesis. Our findings provide a clear example of a noncoding polymorphism that affects a phenotype by modulating a developmental gene regulatory network.
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“MITF, the transcription factor known as the “master regulator of melanogenesis” due to its ability to activate many melanocyte-specific genes (Praetorius et al., 2013), recruits critical components of the SWI/SNF chromatin remodeling complex (including SMARCA2), to the promoter region of its targets (Vachtenheim et al., 2010).”
From An Unexpectedly Complex Architecture for Skin Pigmentation in Africans (2017) · cites this paper as Praetorius et al., 2013
In the citing paper
“The intronic IRF4 variant rs12203592 influences skin pigmentation, tanning response, and hair pigmentation, but shows weaker evolutionary signals than the major sweep loci ( Praetorius et al., 2013 ).”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Praetorius et al., 2013
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“resource for biomedical researchers (Maurano et al., 2012; Hnisz et al., 2013; Weedon et al., 2014; Praetorius et al., 2013).”
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“The rs12203592 C>T polymorphism leads to reduced IRF4 gene expression and consequently reduced TYR expression, leading to sun sensitivity and blue eyes [53].”
BackgroundMethod
Metadata
- Authors
- Praetorius, C., Grill, C., Stacey, S. N., Metcalf, A. M., Gorkin, D. U., Robinson, K. C., Van Otterloo, E., Kim, R. S. Q., Bergsteinsdottir, K., Ogmundsdottir, M. H., Magnusdottir, E., Mishra, P. J., Davis, S. R., Guo, T., Zaidi, M. R., Helgason, A. S., Sigurdsson, M. I., Meltzer, P. S., Merlino, G., Petit, V., Larue, L., Loftus, S. K., Adams, D. R., Sobhiafshar, U., Emre, N. C. T., Pavan, W. J., Cornell, R., Smith, A. G., McCallion, A. S., Fisher, D. E., Stefansson, K., Sturm, R. A., & Steingrimsson, E.
- Affiliations
- University of Iceland (IS)
- deCODE Genetics (Iceland) (IS)
- The University of Queensland (AU)
- Johns Hopkins University (US)
- Harvard University (US)
- National Institutes of Health (US)
- Institut Curie (FR)
- Boğaziçi University (TR)
- University of Iowa (US)
- ORCID
- Praetorius, Christian
- Stacey, Simon N.
- Gorkin, David U.
- Robinson, Kathleen C.
- Ogmundsdottir, Margret H.
- Davis, Sean R.
- Guo, Theresa
- Zaidi, M. Raza
- Helgason, Agnar S.
- Sigurdsson, Martin I.
- Meltzer, Paul S.
- Merlino, Glenn
- Larue, Lionel
- Loftus, Stacie K.
- Adams, David R.
- Sobhiafshar, Ulduz
- Emre, N.C. Tolga
- Pavan, William J.
- Cornell, Robert
- Smith, Aaron G.
- McCallion, Andrew S.
- Fisher, David E.
- Sturm, Richard A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-11
- Volume
- 155
- Issue
- 5
- Pages
- 1022-1033
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3873608
- OpenAlex
- W2034575591
- Cited by
- 228
- References
- 67
- Citations by year
- 2026: 9 · 2025: 18 · 2024: 17 · 2023: 17 · 2022: 22 · 2021: 18 · 2020: 22 · 2019: 15 · 2018: 22 · 2017: 20 · 2016: 13 · 2015: 18 · 2014: 16 · 2013: 1
- FWCI
- 9.28
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- ORBi (University of Liège) (submittedVersion, other-oa)
- Funders
- National Science Foundation
- Melanoma Research Alliance
- Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
- Háskóli Íslands
- Institut National Du Cancer
- National Institutes of Health
- National Cancer Institute (K22CA163799, P01CA163222)
- National Institute of General Medical Sciences (GM071648, T32GM007814, R01GM071648)
- National Institute of Neurological Disorders and Stroke (R01NS062972, NS062972)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR062547, R01AR043369)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Melanoma and MAPK Pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- IRF4, melanogenesis, skin pigmentation, tyrosinase, MITF, TFAP2A, transcriptional regulation, sun sensitivity, freckles, eye color, hair color, gene regulatory networks, zebrafish, mice
- MeSH terms
- Interferon Regulatory Factor-4, Animals, Base Sequence, Enhancer Elements, Genetic, Humans, Melanocytes, Molecular Sequence Data, Pigmentation, Zebrafish, Signal Transduction, Polymorphism, Single Nucleotide, Transcription Factor AP-2, Interferon Regulatory Factors, Mice
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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