BMC Genomics 2009, 10:576 http://www.biomedcentral.com/1471-2164/10/576 YFYig1ubreind5ing sites within the ORFs of the olfactory receptor and histone 4 gene families YY1 binding sites within the ORFs of the olfactory receptor and histone 4 gene families. Four examples of olfac- tory receptor genes and histone 4 genes are shown with the location and direction of their YY1 binding sites. Large gray boxes indicate open reading frames (ORFs) of these single exon genes. Boxes above each ORF show forward direction (empty box) and reverse direction (filled box) of the YY1 binding sites. The arrows in each ORF represent transcriptional directions. The bottom plot shows amino acid sequence identity for all members of each family. A total of 1,178 olfactory receptor proteins have 35% sequence identity (the four shown have 52%) while six genes of the histone 4 family share 95% identity. Conservation of position of YY1 binding sites is non-existent in olfactory genes while it is perfectly preserved in the histone 4 gene family. Directional bias in olfactory genes reflected in the figure is consistent with the complete dataset which yields 3.4 forward sites for every reverse site per 1 kb. The dipeptides encoded by the core motif of the YY1 binding site are identical for all six homologs of the histone 4 gene family (four shown). Olfactory receptor genes, by contrast, have a high number of YY1 binding sites that do not correlate to the position of these dipeptides. fied YY1 binding motifs remains to be demonstrated in vivo, it is plausible that some functional constraints serve to maintain the YY1 binding motifs within the protein- coding regions of the OLFR genes. In one scenario these motifs might be linked to the sudden expansion of this gene family in mammalian genomes. The copy number of the OLFR genes has increased dramatically in recent evo- lutionary times in mammalian genomes, providing a large number of receptor proteins for airborne scents [13]. The clustering of the OLFR genes in chromosomal regions also suggests this gene family may have been duplicated through in situ tandem duplications [13]. Tandem dupli- cation is known to be the most frequent mechanism in increasing copy numbers for gene families [32]. However, it is not well understood how this mechanism carries over the proper information for the transcriptional regulation of duplicated gene copies. In the case of the mammalian OLFR genes, their protein-coding regions may have both information for codon and cis-regulatory elements so that the duplication of these genes would most likely guaran- tee their coding potential as well as associated transcrip- tional control. This might have been one functional constraint for the co-evolution of the YY1 binding motifs within the protein-coding potential of the OLFR genes. Conclusion The current study reports that an unusual enrichment of YY1 binding sites, 4-8 binding sites per gene, are located in the coding regions of olfactory receptor genes in mam- mals. According to statistical analyses, these YY1 binding sites most likely have been selected as cis-regulatory ele- ments. Also, similar patterns are found in other mam- mals, but not in fish, suggesting a mammalian-specific phenomenon. This study further suggests YY1 or YY1- related transcription factors as regulators of mammalian OLFR genes. Methods Visualization of YY1 binding sites in coding regions A custom Perl script, matrix-bidirectional.pl, was run against mouse chromosome files available from Ensem- ble (version NCBIM37.49) ftp://ftp.ensembl.org/pub/ current_fasta/mus_musculus/dna/ (see Additional file 1) [34]. The program calculates score by matching a 10 bp Page 8 of 10 (page number not for citation purposes)