title: Haplotype and diplotype analyses of variation in ERCC5 transcription cis-regulation in normal bronchial epithelial cells.
abstract: Excision repair cross-complementation group 5 (ERCC5) gene plays an important role in nucleotide excision repair, and dysregulation of ERCC5 is associated with increased lung cancer risk. Haplotype and diplotype analyses were conducted in normal bronchial epithelial cells (NBEC) to better understand mechanisms responsible for interindividual variation in transcript abundance regulation of ERCC5 We determined genotypes at putative ERCC5 cis-regulatory SNPs (cis-rSNP) rs751402 and rs2296147, and marker SNPs rs1047768 and rs17655. ERCC5 allele-specific transcript abundance was assessed by a recently developed targeted sequencing method. Syntenic relationships among alleles at rs751402, rs2296147, and rs1047768 were assessed by allele-specific PCR followed by Sanger sequencing. We then assessed association of ERCC5 allele-specific expression at rs1047768 with haplotype and diplotype structure at cis-rSNPs rs751402 and rs2296147. Genotype analysis revealed significantly (P < 0.005) higher interindividual variation in allelic ratios in cDNA samples relative to matched gDNA samples at both rs1047768 and rs17655. By diplotype analysis, mean expression was higher at the rs1047768 alleles syntenic with rs2296147 T allele compared with rs2296147 C allele. Furthermore, mean expression was lower at rs17655 C allele, which is syntenic with G allele at a linked SNP rs873601 (D' = 0.95). These data support the conclusions that in NBEC, T allele at SNP rs2296147 upregulates ERCC5, variation at rs751402 does not alter ERCC5 regulation, and that C allele at SNP rs17655 downregulates ERCC5 Variation in ERCC5 transcript abundance associated with allelic variation at these SNPs could result in variation in NER function in NBEC and lung cancer risk.
authors.affiliation: Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio;
authors.forename: Xiaolu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio;
authors.forename: Erin L
authors.initials: EL
authors.lastname: Crawford
authors.affiliation: Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio;
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Blomquist
authors.affiliation: Departments of Medicine and Public Health and Homeland Security, University of Toledo Health Science Campus, Toledo, Ohio; and.
authors.forename: Sadik A
authors.initials: SA
authors.lastname: Khuder
authors.affiliation: Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio;
authors.forename: Jiyoun
authors.initials: J
authors.lastname: Yeo
authors.affiliation: Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan.
authors.forename: Albert M
authors.initials: AM
authors.lastname: Levin
authors.affiliation: Division of Pulmonary/Critical Care and Sleep Medicine, Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio; Department of Pathology, University of Toledo Health Sciences Campus, Toledo, Ohio; James.Willey2@utoledo.edu.
authors.forename: James C
authors.initials: JC
authors.lastname: Willey
mesh_terms: D000368:Aged; D000483:Alleles; D001980:Bronchi / Q000378:metabolism*; D016022:Case-Control Studies; D004268:DNA-Binding Proteins / Q000235:genetics*; D004720:Endonucleases / Q000235:genetics*; D004847:Epithelial Cells / Q000378:metabolism*; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009687:Nuclear Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics; D000099250:DNA Excision Repair Protein ERCC-5
chemical_list: D004268:DNA-Binding Proteins; D004720:Endonucleases; D009687:Nuclear Proteins; D014157:Transcription Factors; D000099250:DNA Excision Repair Protein ERCC-5
keywords: RNA-sequencing; allele-specific expression; lung cancer; single-nucleotide polymorphism