Bioinformatic and molecular analysis of olfactory receptor gene regulation in zebrafish

Abstract

In vertebrates, an individual olfactory sensory neuron (OSN) expresses only one allele of one olfactory receptor (OR) gene from a huge genomic repertoire. The molecular mechanism governing “one neuron-one receptor rule” are not fully understood and may be regulated by a combination of a variety of cellular mechanisms. Two OR locus-related regulatory mechanisms previously identified are the interaction of transcription factors with specific DNA-binding motifs as a short-range control and the activity of Locus Control Regions as long-range control. Curiously, several regulatory motifs such as Olf1/Ebf1, homeodomain (Lhx2/Emx2) and BPTF motifs were identified in promoter and LCR regions of mice. Here, RNA-Sequencing and bioinformatic analysis were performed in order to detect conserved regulatory motifs within zebrafish OR promoters. Transcript structures and expression levels of OR repertoire were obtained by analysis of transcriptome data. Also, TSS of 161 OR genes were resolved and promoter regions directly upstream of TSSs were identified. De novo motif search with motif-finding bioinformatic tools resulted in a zebrafish-specific motif which is highly similar to Ebf1. Investigation of known regulatory motifs Ebf1, TBP, Lhx2, Emx2 and BPTF indicated presence and distribution of these motifs in OR promoters. Next, a member of highly expressed OR gene family, OR132-5, was investigated with in situ hybridization and a correlation between FPKM levels and number of OSNs that express a given OR was observed. Furthermore, a candidate regulatory motif was identified in this highly expressed OR gene family.