Mechanisms of differential expression of the CYP2A13 7520C and 7520G alleles in human lung: allelic expression analysis for CYP2A13 heterogeneous nuclear RNA, and evidence for the involvement of multiple cis-regulatory single nucleotide polymorphisms

Pharmacogenet Genomics. 2009 Nov;19(11):852-63. doi: 10.1097/FPC.0b013e3283313aa5.


Objective: To identify the mechanisms underlying the decreased allelic expression of a common CYP2A13 allele (7520C>G) in the human lung; CYP2A13 is expressed selectively in the respiratory tract, and is highly efficient in the metabolic activation of several chemical carcinogens.

Methods: The 7520C/G alleles were compared for mRNA stability in cells and relative heterogeneous nuclear RNA (hnRNA) levels in human lungs. Promoter region single nucleotide polymorphisms (SNPs) were identified and analyzed through in-vitro reporter gene assays and gel-shift assays, to uncover the causative SNPs responsible for the decreased allelic expression.

Results: (i) The 7520C>G SNP does not influence CYP2A13 mRNA stability in CYP2A13-transfected human lung or nasal epithelial cells; (ii) levels of the 7520G hnRNA were consistently lower (<10%) than the levels of the 7520C hnRNA in lung samples from nine heterozygous individuals; (iii) three SNPs (-1479T>C, -3101T>G, and -7756G>A) in linkage disequilibrium with the 7520C>G variation were found to cause altered interaction with DNA-binding proteins and decreases in promoter activity; (iv) the suppressive effects of the -1479T>C, -3101T>G, and -7756G>A SNPs on the CYP2A13 promoter were additive, whereas the negative effects of the -1479T>C SNP were enhanced by methylation of -1479C.

Conclusion: The decrease in the expression of 7520G allele was because of the cumulative suppressive effects of multiple SNPs, with each by itself having a relatively small effect on CYP2A13 transcription.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alleles*
  • Aryl Hydrocarbon Hydroxylases / genetics*
  • Aryl Hydrocarbon Hydroxylases / metabolism
  • Base Sequence
  • Cell Line, Tumor
  • Child
  • Child, Preschool
  • DNA Methylation / genetics
  • Electrophoretic Mobility Shift Assay
  • Female
  • Gene Expression Regulation, Enzymologic*
  • Genes, Reporter / genetics
  • Humans
  • Infant
  • Lung / enzymology*
  • Male
  • Molecular Sequence Data
  • Polymorphism, Single Nucleotide / genetics*
  • Pregnancy
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • RNA Stability
  • RNA, Heterogeneous Nuclear / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcription, Genetic


  • RNA, Heterogeneous Nuclear
  • RNA, Messenger
  • Aryl Hydrocarbon Hydroxylases
  • CYP2A13 protein, human