Deciphering the molecular principles of olfactory receptor gene choice

Research Summary The molecular mechanisms by which a finite genome generates an almost infinite ensemble of cellular identities are poorly understood. The mammalian olfactory epithelium provides an extreme example of cellular heterogeneity in which the functional identity of each olfactory sensory neuron (OSN) is determined by the identity of the olfactory receptor (OR) it expresses. In the mouse each OSN expresses only one out of more than a thousand OR genes in seemingly stochastic and monoallelic fashion. Although some of the regulatory layers governing this remarkable process were recently elucidated, important questions remain open. For example, we previously showed that the transcriptionally active OR allele associates with an intricate interchromosomal hub that contains intergenic OR enhancers from many chromosomes. Here, we seek to elucidate the molecular signatures that distinguish intergenic OR enhancers and promoters from the rest of the genome, allowing the formation of specific genomic interactions that culminate in robust OR transcription. Using ATAC-seq and ChIP-seq approaches in FACsorted olfactory neurons, we identified a novel genetic signature that is highly enriched on intergenic OR enhancers and likely promotes the cooperative binding of transcription factors (TFs) that occupy most OR enhancers. Cooperative TF binding on this novel motif likely permits the synergistic recruitment of two distinct types of adaptor proteins to intergenic OR enhancers, creating a unique molecular surface that may dictate the specificity on enhancer-enhancer and enhancer- promoter interactions in the OR subgenome. We therefore propose genetic experiments that will test these predictions and will elucidate the specificity by which intergenic OR enhancers become recognized by TFs, the specificity by which OR enhancers interact with each other and the specificity by which they recruit OR promoters. Because the proteins we propose to investigate are expressed in many neuronal tissues, the regulatory principles that will produced by these studies are likely to impact our general understanding of the combinatorial control of neuronal specification.