Korean J Physiol Pharmacol.  2014 Apr;18(2):169-175. 10.4196/kjpp.2014.18.2.169.

Identification and Functional Characterization of Novel Genetic Variations in the OCTN1 Promoter

• Park HJ
• Choi JH

• KMID: 2285507
• DOI: http://doi.org/10.4196/kjpp.2014.18.2.169

Abstract

Human organic cation/carnitine transporter 1 (OCTN1) plays an important role in the transport of drugs and endogenous substances. It is known that a missense variant of OCTN1 is significantly associated with Crohn's disease susceptibility. This study was performed to identify genetic variants of the OCTN1 promoter in Korean individuals and to determine their functional effects. First, the promoter region of OCTN1 was directly sequenced using genomic DNA samples from 48 healthy Koreans. OCTN1 promoter activity was then measured using a luciferase reporter assay in HCT-116 cells. Seven variants of the OCTN1 promoter were identified, two of which were novel. There were also four major OCTN1 promoter haplotypes. Three haplotypes (H1, H3, and H4) showed decreased transcriptional activity, which was reduced by 22.9%, 23.0%, and 44.6%, respectively (p<0.001), compared with the reference haplotype (H2). Transcription factor binding site analyses and gel shift assays revealed that NF-Y could bind to the region containing g.-1875T>A, a variant present in H3, and that the binding affinity of NF-Y was higher for the g.-1875T allele than for the g.-1875A allele. NF-Y could also repress OCTN1 transcription. These data suggest that three OCTN1 promoter haplotypes could regulate OCTN1 transcription. To our knowledge, this is the first study to identify functional variants of the OCTN1 promoter.

Keyword

Genetic variation; NF-Y; OCTN1; Promoter; Transcriptional regulation

MeSH Terms

Alleles
Binding Sites
Crohn Disease
DNA
Genetic Variation*
Haplotypes
HCT116 Cells
Humans
Luciferases
Promoter Regions, Genetic
Transcription Factors
DNA
Luciferases
Transcription Factors

Figure

• 

  Fig. 1 Effect of variants on OCTN1 promoter activity. Promoter activities were measured 30 h after the transfection of reporter plasmids containing the major OCTN1 haplotypes (a) or genetic variants (b) into HCT-116 cells. The reporter activity of each construct was compared with empty vector (a, EV, pGL4.11b[luc2]) or the reference haplotype (b, H2). The data represent mean±SD of triplicate wells in a representative experiment. ***p<0.001.

• 

  Fig. 2 Electrophoretic mobility shift analysis of the OCTN1 reference and g.-1875T>A variant sequences. (a) Labeled oligonucleotides (NF-Y consensus, lanes 1~3; OCTN1 reference, lanes 4~6; variant, lanes 7~9) were incubated with 35µg of nuclear protein extracts. Competition assays were performed using unlabeled NF-Y consensus (lanes 2, 5, and 8) or mutant (lanes 3, 6, and 9) oligonucleotides. The arrow indicates the position of the DNA-protein complex. (b) Labeled oligonucleotides (NF-Y consensus, lanes 1~3; OCTN1 reference, lane 4; variant, lane 5) were incubated with 20µg of nuclear protein extracts. Supershift assays were performed using a mixture of three different antibodies against NF-Y (lanes 2, 4, and 5) or an antibody against MZF-1 (lane 3).

• 

  Fig. 3 Effect of NF-Y on OCTN1 promoter activity. Promoter activities were measured 30 h after the co-transfection of reference or variant reporters and varying amounts of NF-Y plasmids into HCT-116 cells. The reporter activity of each construct was compared with naïve promoter activity. The data represent mean±SD of triplicate wells in a representative experiment. *p<0.05, ***p<0.001 vs. naïve promoter activity and †p<0.01 vs. reference promoter activity.

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