BMC Genomics BioMed Central Research article YY1's DNA-Binding motifs in mammalian olfactory receptor genes Christopher D Faulk and Joomyeong Kim* Open Access Address: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA Email: Christopher D Faulk - cfaulk1@tigers.lsu.edu; Joomyeong Kim* - jkim@lsu.edu * Corresponding author Published: 3 December 2009 BMC Genomics 2009, 10:576 doi:10.1186/1471-2164-10-576 This article is available from: http://www.biomedcentral.com/1471-2164/10/576 Received: 21 April 2009 Accepted: 3 December 2009 © 2009 Faulk and Kim; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: YY1 is an epigenetic regulator for a large number of mammalian genes. While performing genome-wide YY1 binding motif searches, we discovered that the olfactory receptor (OLFR) genes have an unusual cluster of YY1 binding sites within their coding regions. The statistical significance of this observation was further analyzed. Results: About 45% of the olfactory genes in the mouse have a range of 4-8 YY1 binding sites within their respective 1 kb coding regions. Statistical analyses indicate that this enrichment of YY1 motifs has likely been driven by unknown selection pressures at the DNA level, but not serendipitously by some peptides enriched within the OLFR genes. Similar patterns are also detected in the OLFR genes of all mammals analyzed, but not in the OLFR genes of the fish lineage, suggesting a mammal-specific phenomenon. Conclusion: YY1, or YY1-related transcription factors, may help regulate olfactory receptor genes. Furthermore, the protein-coding regions of vertebrate genes can contain cis-regulatory elements for transcription factor binding as well as codons. Background The transcription factor YY1 is a Gli-Kruppel type zinc fin- ger protein that is highly conserved from insects through vertebrates [1]. YY1 can function as an activator, repressor, or initiator depending upon the other regulatory elements in the region [2]. YY1 also interacts with a variety of pro- teins including components of RNA polymerase II com- plex, transcription factors, and histone-modifying complexes [3-5]. According to genome-wide surveys, about 10% of all human genes contain YY1 binding motifs in their promoter regions [6]. Functionally, YY1 is involved in many biological processes, including embry- onic development, cell cycle progression, apoptosis, B cell development, Polycomb group Gene (PcG)-mediated repression, genomic imprinting, and X chromosomal inactivation [2,3,7]. YY1 was also initially identified as a factor controlling the transcriptional activity of the murine retrotransposon 'Intracisternal A Particle' [8]. Since then, many retroposons, including SINE, LINE, and endogenous retrovirus families, have been shown to con- tain YY1 binding sites in their promoter regions [3,4]. Due to this ubiquitous presence of YY1 binding sites in genome-wide repeats, YY1 has also been regarded as a sur- veillance gene that is responsible for repressing transcrip- tional background noise from these repeats [9]. The olfactory receptor (OLFR) genes of mammals encode short, single coding exon, G protein-coupled receptors that are responsible for sensing a large number of air- borne scents [10]. This gene family is comprised of over 800 and 1,300 gene members in human and mouse respectively, forming the largest gene family in mamma- Page 1 of 10 (page number not for citation purposes)