The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

PLoS One. 2017 Feb 24;12(2):e0172681. doi: 10.1371/journal.pone.0172681. eCollection 2017.


We studied functional effect of rs12722489 single nucleotide polymorphism located in the first intron of human IL2RA gene on transcriptional regulation. This polymorphism is associated with multiple autoimmune conditions (rheumatoid arthritis, multiple sclerosis, Crohn's disease, and ulcerative colitis). Analysis in silico suggested significant difference in the affinity of estrogen receptor (ER) binding site between alternative allelic variants, with stronger predicted affinity for the risk (G) allele. Electrophoretic mobility shift assay showed that purified human ERα bound only G variant of a 32-bp genomic sequence containing rs12722489. Chromatin immunoprecipitation demonstrated that endogenous human ERα interacted with rs12722489 genomic region in vivo and DNA pull-down assay confirmed differential allelic binding of amplified 189-bp genomic fragments containing rs12722489 with endogenous human ERα. In a luciferase reporter assay, a kilobase-long genomic segment containing G but not A allele of rs12722489 demonstrated enhancer properties in MT-2 cell line, an HTLV-1 transformed human cell line with a regulatory T cell phenotype.

MeSH terms

  • Alleles
  • Base Sequence
  • Binding Sites
  • Cell Line, Transformed
  • Chromatin Immunoprecipitation
  • Electrophoretic Mobility Shift Assay
  • Estrogen Receptor alpha / genetics*
  • Estrogen Receptor alpha / metabolism
  • Gene Expression Regulation
  • Genes, Reporter
  • Human T-lymphotropic virus 1 / genetics
  • Humans
  • Interleukin-2 Receptor alpha Subunit / genetics*
  • Interleukin-2 Receptor alpha Subunit / metabolism
  • Introns
  • Luciferases / genetics
  • Luciferases / metabolism
  • Polymorphism, Single Nucleotide*
  • Protein Binding
  • Response Elements*
  • T-Lymphocytes, Regulatory / cytology
  • T-Lymphocytes, Regulatory / metabolism*


  • Estrogen Receptor alpha
  • IL2RA protein, human
  • Interleukin-2 Receptor alpha Subunit
  • Luciferases

Grant support

This work was supported by Russian Science Foundation (, grant # 14-14-01140 to DVK. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.