Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray

Abstract

Background: Olfactory receptor (OR) genes were discovered more than a decade ago, when Buck and Axel observed that, in rats, certain G-protein coupled receptors are expressed exclusively in the olfactory epithelium. Subsequently, protein sequence similarity was used to identify entire OR gene repertoires of a number of mammalian species, but only in mouse were these predictions followed up by expression studies in olfactory epithelium. To rectify this, we have developed a DNA microarray that contains probes for most predicted human OR loci and used that array to examine OR gene expression profiles in olfactory epithelium tissues from three individuals.

Results: We detected expression of 437 (76%) human OR genes in these olfactory epithelia. Interestingly, we detected widespread expression of OR pseudogenes, an observation that may shed light on the mechanism of OR gene choice in the olfactory sensory neurons. To address the hypothesis that OR genes may carry out additional functions, we also characterized the expression of OR genes in a number of non-olfactory tissues.

Conclusion: While our results corroborate the functional annotation of the majority of predicted human odorant receptors, we find that a large number of putative human OR genes are expressed in non-olfactory tissues, sometimes exclusively so. Our evolutionary analysis of ectopically expressed human OR genes does not lend support to the hypothesis that these genes have alternative functions.

Figure 1

Gel electrophoresis of PCR amplification results using cDNA from three olfactory epithelium tissues, heart, testis, liver, lung, and kidney as template. (a) The 440 base-pair (bp) OBP2B product was only amplified from the olfactory epithelium samples. (b) The 562 bp cathepsin C (CTSC) product was successfully amplified from all three samples. Both primer pairs were designed to amplify multiple exon products and hence are expected to yield a much larger product (1,686 bp) if genomic DNA was used as template. (c) The 378 bp product of the OMP gene was amplified from the olfactory epithelium samples to confirm that these samples contain neutrons.

Figure 2

Expression profile of human OR genes across tissues. The log transformed detection P values for OR genes in all tissues (from Additional data file 1) were standardized to have mean 0 and standard deviation 1 and are color coded (red and blue shades indicate values above and below the mean, respectively). The dendrograms on top of each panel illustrate the clustering (by hierarchical clustering in dchip [48]) of tissue samples based on the profile of OR gene expression. (a) All 578 predicted OR genes are included in a comparison between olfactory epithelium (OE) and the non-olfactory tissues (see Materials and methods). (b) Shown are the data for only the 147 OR genes with significantly elevated expression in non-olfactory tissues.

Figure 3

The number of predicted human OR genes whose expression was detected (at P < 0.05) in one or more of the three olfactory epithelium (OE) samples. As can be seen, there is a substantial difference in the expressed OR gene repertoire of each of the three OE samples.