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Open Access Research article

Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs

Janet M Young1*, Ralf M Luche12 and Barbara J Trask1

Author Affiliations

1 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

2 Present address: Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

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BMC Genomics 2011, 12:561  doi:10.1186/1471-2164-12-561

Published: 15 November 2011

Abstract

Background

Mammalian olfactory receptors (ORs) are subject to a remarkable but poorly understood regime of transcriptional regulation, whereby individual olfactory neurons each express only one allele of a single member of the large OR gene family.

Results

We performed a rigorous search for enriched sequence motifs in the largest dataset of OR promoter regions analyzed to date. We combined measures of cross-species conservation with databases of known transcription factor binding sites and ab initio motif-finding algorithms. We found strong enrichment of binding sites for the O/E family of transcription factors and for homeodomain factors, both already known to be involved in the transcriptional control of ORs, but did not identify any novel enriched sequences. We also found that TATA-boxes are present in at least a subset of OR promoters.

Conclusions

Our rigorous approach provides a template for the analysis of the regulation of large gene families and demonstrates some of the difficulties and pitfalls of such analyses. Although currently available bioinformatics methods cannot detect all transcriptional regulatory elements, our thorough analysis of OR promoters shows that in the case of this gene family, experimental approaches have probably already identified all the binding factors common to large fractions of OR promoters.

Keywords:
Olfactory receptor; comparative genomics; transcriptional regulation; transcription factor binding site; position weight matrix; homeodomain