Mechanisms of allergy and clinical immunology
Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)

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Background

Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.

Objective

Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels—rs3765526, rs9526569, and rs1046295—for a role in transcription factor binding.

Methods

We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.

Results

Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10−16), preferential expression of the A allele consistent with a functional role for rs1046295.

Conclusion

These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.

Section snippets

Subjects

Allele-specific expression analysis was performed in a subset of the MRC-A population, MRC-A/RNA. The MRC-A panel consists of 200 families of British descent recruited through a proband between the ages of 5 and 18 years with severe asthma, defined as 1 or more hospital admissions caused by asthma and taking maintenance-inhaled steroids. Both parents and at least 1 sibling were included for each family, regardless of disease status. EBV immortalized lymphoblastoid cell lines were created from

Bioinformatic analysis of transcription factor binding of 3 PHF11 SNPs

The sequences immediately flanking rs3765526, rs9526569 and rs1046295 were interrogated in silico for potential transcription factor binding sequences by using the programs TFSearch, TFScan, and MatInspector (Genomatix Software GmbH). A number of transcription factor binding sites were predicted to span each SNP with several instances of potential allele-specific binding (Table I).

For rs3765526, 5 transcription factors were predicted to bind specifically only to 1 allele (allele A: VBP, E4BP4,

Discussion

Previous positional cloning of chromosome 13q14 implicated PHF11 as a determinant of total serum IgE levels, although because of the possibility of a joint SETDB2-PHF11 transcript and further distant alleles affecting linkage, all 3 genes in the region, SETDB2, PHF11, and RCBTB1, could influence asthma susceptibility.13 Here we have shown by EMSA experiments that the A allele of rs1046295 is capable of interacting with the transcription factor Oct-1 with greater affinity than the alternate G

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    Supported by the Wellcome Trust (075491/Z/04).

    Disclosure of potential conflict of interest: The authors have declared that they have no conflict of interest.

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