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Gene expression

Looping together the functions of SNPs

Nature Reviews Genetics volume 13, pages 148–149 (2012)Cite this article

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The authors' starting point was SNP rs12913832, which is known to be highly associated with human eye, hair and skin colour. Genotyping of neonatal primary human epidermal melanocytes from lightly pigmented donors (HEMnLP cells) and darkly pigmented donors (HEMnDP cells) indicated that the HEMnLP cells are homozygous for the rs12913832 C allele and that the HEMnDP cells are homozygous for the T allele. The SNP resides 21 kb upstream of the oculocutaneous albinism 2 (OCA2) promoter — OCA2 protein is known to have a role in human pigmentation — in an intron of another gene (namely, hect domain and RLD 2 (HERC2)). The authors found that HEMnLP cells have lower gene expression and lower recruitment of RNA polymerase II than the HEMnDP cells.

These results suggested that the rs12913832 region might be a long range enhancer that regulates expression of OCA2. To explore this possibility, Visser et al. looked for open chromatin — a characteristic of enhancers — using formaldehyde-assisted identification of regulatory elements (FAIRE), looked at histone modifications that are typical of enhancers and tested the enhancer activity of the region in a luciferase assay. They found evidence of a melanocyte-specific enhancer in the rs12913832 region and showed that HEMnDP cells (which have the T allele) have stronger enhancer signals and activity than HEMnLP cells.

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References

ORIGINAL RESEARCH PAPER

  1. Visser, M., Kayser, M. & Palstra, R.-J. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin loop formation between a long-range enhancer and the OCA2 promoter. Genome Res. 10 Jan 2012 (doi:10.1101/gr.128652.111)

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FURTHER READING

  1. Ong, C.-T. & Corces, V. G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nature Rev. Genet. 12, 283–293 (2011)

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Authors
  1. Hannah Stower
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Stower, H. Looping together the functions of SNPs. Nat Rev Genet 13, 148–149 (2012). https://doi.org/10.1038/nrg3180

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