Distinctive distribution of AIM1 polymorphism among major human populations with different skin color

Nakayama, Kazuhiro; Fukamachi, Shoji; Kimurâ, Hiroshi; Koda, Yoshiro; Soemantri, Augustinus; Ishida, Takafumi

doi:10.1007/s100380200007

Cited by 57 publications

(61 citation statements)

References 6 publications

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“…Both RNA-Seq and qPCR results showed similar fold changes and confirmed our previous observations that SLC45A2 (OCA4) is expressed at significantly higher levels in HEM-L. P-protein (OCA2) was found to be higher in HEM-D by qPCR (consistent with previous studies [22, 68]) as well as SLC24A5 (OCA6), but the difference was not statistically different by RNA-Seq. Interestingly, the SLC45A2 mRNA found in the HEM-L libraries was exclusively accounted for by the 374F allele, while HEM-D libraries contained the 374L allele, in agreement with previous findings [20-22]. …”

Section: Resultssupporting

confidence: 92%

“…Recent studies suggested that different pigmentation phenotypes could be the result of various combinations of single nucleotide polymorphisms (SNPs) in some pigmentation genes [19]. One particular SNP resulting in a point mutation in the melanosomal protein mutated in oculocutaneous albinism IV (OCA4 or SLC45A2) shows strong correlation with skin color [20, 21]. Moreover, the mRNA for the allele present in light skin was found to be higher than the allele present in dark skin [22].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide transcriptome analysis of human epidermal melanocytes

Haltaufderhyde

Oancea

2014

Genomics

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Because human epidermal melanocytes (HEMs) provide critical protection against skin cancer, sunburn, and photoaging, a genome-wide perspective of gene expression in these cells is vital to understanding human skin physiology. In this study we performed high throughput sequencing of HEMs to obtain a complete data set of transcript sizes, abundances, and splicing. As expected, we found that melanocyte specific genes that function in pigmentation were among the highest expressed genes. We analyzed receptor, ion channel and transcription factor gene families to get a better understanding of the cell signalling pathways used by melanocytes. We also performed a comparative transcriptomic analysis of lightly versus darkly pigmented HEMs and found 16 genes differentially expressed in the two pigmentation phenotypes; of those, only one putative melanosomal transporter (SLC45A2) has known function in pigmentation. In addition, we found 166 genes with splice isoforms expressed exclusively in one pigmentation phenotype, 17 of which are genes involved in signal transduction. Our melanocyte transcriptome study provides a comprehensive view and may help identify novel pigmentation genes and potential pharmacological targets.

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Section: Resultssupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Genome-wide transcriptome analysis of human epidermal melanocytes

Haltaufderhyde

Oancea

2014

Genomics

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“…A similar pattern can be observed at rs16891982 in SLC45A2 [23], which has been reported to be associated with pigmentation in several species, e.g., mice, fish, birds, and horses [24–26]. Other variants in this gene, including rs26722, rs2287949, and rs40132, were also shown to be coloration-associated in Europeans [23, 27, 28]. Another important pigmentation-related gene identified in European is MC1R [29–31].…”

Section: Introductionsupporting

confidence: 60%

Adaptation of human skin color in various populations

Deng

2017

Hereditas

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BackgroundSkin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine.DiscussionImpressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies.ConclusionPrevious studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.

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“…Several studies have reported polymorphisms in SLC45A2 with significant allele frequency differences between major human populations [34],[35]. Graf et al [14] were the first to reveal an association between SLC45A2 alleles and intrapopulation pigmentation variation based on E272K and L374F allele frequency differences, showing that alleles 374L and 272K were significantly associated with dark hair, skin, and eye color in North Europeans.…”

Section: Discussionmentioning

confidence: 99%

The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population

et al. 2014

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We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans.

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Distinctive distribution of AIM1 polymorphism among major human populations with different skin color

Cited by 57 publications

References 6 publications

Genome-wide transcriptome analysis of human epidermal melanocytes

Genome-wide transcriptome analysis of human epidermal melanocytes

Adaptation of human skin color in various populations

The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population

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