Human Molecular Genetics

Human Molecular Genetics 2005 14(Review Issue 1):R33-R39; doi:10.1093/hmg/ddi105

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Regulation of odorant receptors: one allele at a time

Benjamin M. Shykind^*

Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA

^* To whom correspondence should be addressed. Email: bs165{at}columbia.edu

Received January 5, 2005; Revised February 16, 2005; Accepted February 23, 2005

	ABSTRACT

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
The odorant receptors (ORs) make up the largest gene family in mammals. Each olfactory sensory neuron chooses just one OR from the more than 1000 possibilities encoded in the genome and transcribes it from just one allele. This process generates great neuronal diversity and forms the basis for the development and logic of the olfactory circuit between the nose and the brain. The mechanism behind this monoallelic regulation has been the subject of intense speculation and increasing experimental investigation, yet remains enigmatic. Recent genetic experiments have brought the outlines of the process into sharper relief, identifying a feedback mechanism in which the first odorant receptor expressed, generates a signal that stabilizes its choice, thus maintaining singular selection. In the absence of this signal, the olfactory neuron re-enters the selection process and switches to choose an alternate OR. Irreversible genetic changes in the nuclei of olfactory neurons do not accompany OR selection, which must therefore be initiated by an epigenetic process that may involve a stochastic mechanism.

	INTRODUCTION

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
The nose recognizes chemical information in the environment and converts it into meaningful neural signal, allowing the brain to discriminate among thousands of odorants and giving the animal its sense of smell. Since the cloning of the olfactory receptor (OR) genes from mammals (1), a molecular logic of olfaction has emerged. In the mouse, the genes that encode the ORs, numbering upwards of 1000 and comprising the largest mammalian gene family, are located in clusters which are scattered throughout the genome (2–4). The existence of such a large complement of receptors suggested that each odor elicits a unique signature, defined by the interactions with a limited number of relatively specific olfactory receptors (1). Together these form a combination of interactions more than sufficient to encode the 104–105 different odors animals may perceive (5). For the brain to determine which odorant is present, it must determine which ORs have been activated and two key properties of the olfactory system facilitate this task. First, each olfactory neuron expresses only one olfactory receptor. Secondly, the axons of neurons expressing that same OR converge to one locus (the glomerulus) in the olfactory bulb, the first relay station of olfactory information in the brain (6–8) (Fig. 1). The brain can therefore determine which receptors have been bound by identifying which glomeruli have been activated. This creates a sensory map in the bulb such that odor quality may be encoded by patterns of spatial activation. This one-to-one correspondence between receptor and glomerulus is critical for the logic of this circuit and is dependent on the correct regulation of the OR gene family, one receptor per neuron.

View larger version (51K): [in this window] [in a new window]   Figure 1. Odorant receptor expression and axonal projections. (A) Whole mount view of a compound heterozygous mouse, age P30, genetically modified (as shown by the schematic constructs) to express tau-lacZ and GFP (15,48) from each allele of the P2 odorant receptor gene through an internal ribosome entry site (i), subject to anti-ß-gal and anti-GFP immunohistochemistry. Neurons express P2 monoallelically (green or red cells) in the olfactory epithelium (oe), and project their axons back into the olfactory bulb (ob) to form a glomerulus (gl, within white box). Nuclei are counterstained by Toto-3 (blue). Images were acquired using a Bio-Rad MRC 1024ES confocal microscope and were assembled with Adobe Photoshop 7.0. (B) High power view of (boxed area in A) the convergence of P2 axons to a glomerulus (gl, red and green fibers). Neighboring glomeruli are indicated by asterisks.

 
Olfactory sensory neurons are regenerated throughout the life of the animal. Thus OR gene selection and expression, which can be detected as early as E11.25 (9), is not synchronized with a developmental stage but rather occurs continuously as the olfactory neurons are born and exit the cell cycle. The mechanism of OR regulation is unknown but recent experiments have shed light on important aspects of the process. Here, the phenomenon of OR regulation will be summarized, models of OR selection will be discussed and recent data about the initiation and maintenance of this singular, mono-allelic odorant receptor choice will be reviewed.

	EMERGENCE OF A REGULATORY PUZZLE

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
The isolation of the OR genes led to a rapid molecular dissection of the biology of olfaction and allowed two fundamental characteristics of OR expression to be revealed by RNA in situ hybridization studies. First, neurons expressing a given receptor are restricted to one of four broad zones running across the olfactory epithelium; and secondly, within a zone, individual receptors are expressed sparsely and without apparent pattern (10–12). Quantitative analysis of these in situ hybridization experiments led to the suggestion that each neuron in the nose expresses only one or a few members of the gene family (11,12). Subsequent analyses of cDNAs synthesized from single olfactory neurons revealed that just a single OR species could be isolated from each cell and strengthened this ‘one neuron–one receptor’ hypothesis (5,13). An intriguing additional phenomenon was uncovered when ORs were shown to be transcribed from just one allele (13). Thus a striking regulatory challenge (hypothesized by Buck and Axel in 1991) exists for the olfactory sensory neuron, which must select a single receptor from just one allele of a spatially allowed subset of a widely dispersed gene family. The logic of the olfactory circuit rests upon this regulatory process as does the formation of the sensory map, which is dependent on receptor protein to guide the path-finding axon (14,15). Aberrant expression of multiple ORs per neuron may disrupt olfactory axon guidance and thus prevent accurate formation of the glomerular map. Importantly, once a neuron establishes its synapse in the olfactory bulb, it must remain committed to its OR, as any change in receptor would change the ligand specificity of the cell and confound the sensory map by inappropriate glomerular activation. Thus OR regulation may be divided into two phases: initiation of selection and maintenance of the choice. What paradigms of gene expression are behind these processes?

	MODELS OF OR GENE CHOICE

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
Two models may be proposed to explain the selection of single OR alleles. In a deterministic model (Fig. 2), individual OR is chosen by the generation of a unique combination of transactivators that activate a single receptor bearing the appropriate cis-acting elements. In this model of gene activation an additional level of regulation, perhaps akin to X-inactivation (16), must be invoked to account for monoallelic expression, as the same combinatorial would activate both copies of the OR. An alternative, stochastic model (Fig. 2) supposes that the choice of receptor is random, resulting from the selection of a machine or process that is itself singular, able to interact with one OR allele at a time. Such an unorthodox mechanism would operate on a cis-acting element common to all OR genes and could generate random OR choice. A series of transgenic experiments in mice have lent support for the stochastic model (17–19). These studies revealed that OR transgenes could recapitulate the pattern of OR expression yet remarkably, expression was exclusive: transgenes and endogenous copies were rarely co-expressed in the same cell (17–19). This phenomenon, which had only previously been observed for the antigen receptor genes (20), is inconsistent with a deterministic mechanism which should co-express the transgene and cognate endogenous alleles. Exclusive expression is even observed between OR transgenes that are differentially marked and located in the same array (19). These data are in contrast with observations in Drosophila, where OR transgenes are co-expressed with their endogenous, cognate copies (21). There are conceivable evolutionary advantages to an OR regulatory mechanism that would generate exclusive expression by default. Such a process would immediately accommodate new receptor genes without the evolution of transactivators with new specificities and their cognate OR promoters. The simple duplication and sequence variation of an OR gene would increase the functional repertoire of receptors. Such a mechanism could have promoted the rapid growth of the OR gene family. Is there evidence for common OR promoter motifs required by the stochastic model? Sequence analyses have been equivocal. Vassalli et al. identified a weakly conserved homeodomain element upstream of the start sites of several OR genes (18). Analysis by Hoppe et al. did not find such elements (22) and Lane et al. failed to find common OR motifs flanking 18 OR genes of the P2 receptor cluster (23), but did identify a common DNA element in front of 73 pheromone receptor genes, which share similar expression phenomena with the ORs. The importance of these elements awaits functional validation. Candidate OR regulatory factors have been identified by one-hybrid experiments and either fail to demonstrate specific control of OR (24) or have not yet been validated in vivo (25).

View larger version (17K): [in this window] [in a new window]   Figure 2. Two models of receptor choice. In the deterministic model (left), individual odorant receptor genes (R1, R2, ..., R1000) are selected by unique combinations of transacting factors (colored spheres) that recognize cognate promoter elements (shown in red, yellow, or green) specific to the OR gene. In the stochastic model (right), individual odorant receptor genes (R1, R2, ..., R1000) are activated by a singular entity, represented by the blue sphere.

 

	STOCHASTIC PROCESSES

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
What types of stochastic processes could generate singular, mono-allelic OR choice? The conceptual and organizational similarities between the odorant receptor and lymphocyte receptor gene families led to the proposal that the olfactory and immune systems may share common regulatory processes. This led to the suggestion that DNA recombination may play a role in the selection of ORs (1). The demonstration that OR expression is mono-allelic and mutually exclusive, made this explanation for OR regulation even more alluring. One recombinational model was envisioned in which a single OR gene would be inserted into a transcriptionally active locus by gene conversion (1,13). This mechanism participates in yeast mating type switching (26,27) and trypanosome variable surface glycoprotein (VSG) expression (28). However, fluorescent in situ hybridization (FISH) studies provide evidence against this model (29). In these experiments, the site of transcription of an OR was localized by RNA FISH using OR intronic sequences as probes. The location of both copies of the OR gene was concomitantly visualized by DNA FISH. In all cases, the site of OR synthesis corresponded to one of the two alleles, suggesting that the selected OR was being transcribed in situ and not from a remote expression site. However, these data can rule out neither the transposition of OR into an active locus nor the transposition of regulatory sequences proximal to an OR. Evidence against these types of recombination was obtained recently by two groups that reported the generation of cloned mice from post-mitotic olfactory neurons (30,31). They reasoned that if the mechanism of receptor selection involve permanent genomic changes in olfactory neurons, then a donor neuron may bestow a restricted genetic potential upon the clone, as was observed in lymphocytes (32). These experiments, using nuclear transfer from olfactory neurons genetically marked to confirm their differentiated state, produced viable, clonal mice that appeared to express the full repertoire of ORs. In addition, the genomic structure around the selected OR locus remained unaltered. Odorant receptor expression thus occurs without irreversible changes to the DNA of olfactory neurons.

Absent DNA recombination governing receptor choice, what types of random, epigenetic processes may explain OR selection? It is possible that a unique locus or factory exists in the nucleus which may accommodate and activate just one OR allele at a time. Such a spatial singularity has been invoked to explain the conceptually similar regulation of the VSG genes in trypanosomes. This mechanism involves the gene conversion of a VSG into just one of 20 expression sites (ES) in the genome. However, the choice of a single VSG is thought to arise from its interaction with the expression site body (ESB), a solitary entity in the nucleus able to interact with just one ES at a time. Switching can occur either by the VSG gene conversion into an ES in the ESB or by the switching of new ES for old into the ESB. OR selection could be accomplished by a similar mechanism, in which an individual OR is transcribed by a single nuclear entity (23,33).

An alternate mechanism of OR choice could involve a rate-limiting process. In such a kinetic singularity model, receptor choice is presumed to be an inefficient process in which only a single OR allele is activated on average during a given developmental window. The cis-acting transcriptional elements associated with each OR gene may generate rare probabilistic expression (34) of ORs in the context of a repressive chromatin environment. Such a model has been proposed to regulate the exclusive, monoallelic expression of antigen receptor genes (35,36).

The possibility of singular OR expression arising from the action of a locus control region (LCR) has been proposed (10,13). Such a mechanism possesses characteristics that may be both spatially and kinetically limiting. Recently, an LCR-like OR control element has been identified (37). Although several groups have reported the expression of OR transgenes containing a few kilobases of 5' flanking DNA (17,18), the MOR28 receptor cluster requires >100 kb of 5' sequence (19). Present in this 100 kb region is a 2 kb element, termed ‘H,’ that is conserved between mice and humans (38) and is required for expression of the MOR28 cluster (37). Interestingly, when the H-element was placed closer to the MOR28 gene in the cluster, it was dramatically over-represented in its zone while downstream neighboring ORs were chosen less frequently (37). The H-element does possess hallmarks of an olfactory LCR but may not be a central modulator of OR regulation. No other OR loci have been shown to possess or require such an element, and it remains unclear whether it is responsible for individual OR choice within the cluster or rather opens an otherwise tightly repressed locus and allows access of a stochastic selection machinery to the OR genes.

	MAINTENANCE OF OR CHOICE

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
Once an OR has been chosen, how does the neuron stay committed to it and prevent the expression of additional receptors? OR choice must be stable in the neuron after it wires to the bulb, as commitment to one receptor is critical for olfactory coding. It must also be stable during axon guidance, when it determines glomerular position. The answer appears to involve feedback repression of the selection process by the first expressed receptor. The existence of this mechanism was recently reported by several groups (37,39–41) who observed it while examining a long-standing conundrum in the field: what is the fate of an olfactory neuron that expresses an odorant receptor pseudogene? The OR gene family is riddled with pseudogenes (2,4), many of which are expressed (42). If neurons that select non-functional ORs are destined to inactivity, then the olfactory epithelium should be a mosaic of functional and non-functional neurons. Alternatively, such choices might doom the cell. The Sakano and Reed groups examined this question by generating mice bearing OR transgenes containing open reading frame deletions and truncations and marked to co-express lacZ or GFP (green fluorescent protein) reporter genes. Neurons that chose these mutant ORs express additional receptors at high frequency and project their axons diffusely in the bulb. In control experiments, cells expressing intact OR transgenes did not show the co-expression of other ORs and their axons converged to a discrete glomerulus. This axon-wandering phenotype was previously observed by Wang et al. in mice bearing a replacement of the P2 receptor with lacZ generated by homologous recombination (15). Feinstein et al. (41) replaced an OR coding region with GFP by homologous recombination and showed that green fluorescent neurons gained promiscuous sensitivity to applied odorants compared with control cells with an intact OR. Taken together, these results suggest a feedback mechanism in which a functional OR mediates the stabilization of receptor choice and maintains its status as the sole expressed OR. A non-functional receptor cannot generate such a signal and the cell may continue to choose until it picks an active OR.

What is the fate of expressed but non-functional OR? The continued expression of the defective receptor after the choice of a functional receptor would be prima facie evidence of bi-allelic transcription and thus inconsistent with a spatial singularity model of OR choice. However, experiments where the expression of the marker protein is dependent on the continued transcription of the mutant OR will not detect cells that shut it down (37,40,41). To circumvent this limitation we used a lineage-marking strategy in which cells that expressed a modified mutant or wild-type OR allele would be permanently marked by Cre-mediated activation of GFP expression from an unlinked reporter (43). Consistent with previous studies demonstrating that deletion of OR coding sequences by homologous recombination leads to sustained decrease in the frequency of cells expressing the mutant OR (15,44,45), we observed a comparable drop in neurons expressing the Cre-substituted allele. Consistent with Sakano and coworkers (37) and Reed and Lewcock (40) we observed efficient selection of alternate ORs in these cells which, when coupled with the shutdown of the mutant allele, amounted to a switching between ORs, rather than their co-expression (39). This lineage-marking strategy also let us examine the stability of functional OR expression. Interestingly, we observed that MOR28 demonstrated instability and switching 10% of the time it was chosen. Thus neurons that choose either mutant or wild-type ORs may switch, albeit with very different rates. Further, switching to a receptor occurs at a frequency similar to that with which it is initially chosen in the epithelium. This suggests that switching represents a re-entry into the selection process and not is mechanistically different than initial choice. The timing of shutoff of the mutant OR allele suggests that switching likely occurs early in the development of sensory neurons, before the OR is required for axon targeting (39).

Thus a model emerges (Fig. 3) in which OR selection is mediated by a stochastic mechanism involving either a singular selection machine or a limiting kinetic process. Initially, receptor expression is unstable, but a functional OR may mediate a feedback stabilization that commits the cell to the receptor. This is analogous to one mechanism of allelic exclusion of antigen receptor genes (20). Non-functional ORs are not able to mediate the feedback signal and switching occurs as the defective allele is shutdown and an alternate OR is chosen. Following receptor stabilization the neuron enters a phase characterized by commitment to one receptor. A generalized repression of all other OR loci at this point may further ensure the expression of just one OR. In this model, ORs may be transcribed serially, one promoter at a time. It remains possible that the phenomenon interpreted as OR co-expression (37,40) in fact represents a failure of the mutant transgenes to shutdown. This could occur if cis-acting control elements are absent from the transgene or if it integrates into a locus in the genome that restricts the full repertoire of OR regulation. The use of homologous modifications of OR loci may more faithfully preserve the facets of an arguably complex regulatory process.

View larger version (22K): [in this window] [in a new window]   Figure 3. Model of OR selection and maintenance. (A) Choice of functional receptor. OR gene is selected by a stochastic mechanism (blue sphere). Receptor protein (green) mediates a feedback that leads to stabilization of receptor choice (symbolized by small red sphere). (B) Choice of non-functional receptor. Non-functional OR gene (with red ‘X’) is selected by a stochastic mechanism (blue sphere). Non-functional OR protein (yellow) fails to mediate stabilization and the non-functional receptor gene is shutdown as switching occurs and the selection process continues until functional OR is chosen.

 
Switching allows the olfactory genome to carry a large number of pseudogenes without deleterious effects. These defective copies may serve to generate new ORs by reversion or gene conversion events. Shutoff of defective alleles, although not required for the generation of monospecific olfactory neurons, may be critical to protect cells from the effects of toxic or interfering products of mutant ORs. Alternatively, switching and shutoff may be concerted as in trypanosome VSG regulation, when alleles exchange places in singular selection machinery. What is the explanation of the switching observed from functional ORs? The proposed early instability of selection inherent in the process means that occasionally, even a functional OR will not reach the threshold level of expression needed to generate a feedback signal, and switching will occur.

	PERSPECTIVES ON MONOALLELISM

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
There are both developmental and perceptual rationales for the olfactory neuron to select just a single receptor gene, yet it is unclear why this expression must also be monoallelic. Is monoallelism an integral part of the mechanism of receptor choice or a consequence of it? In a deterministic model of OR expression, there would be no mechanistic requirement for monoallelism. Rather, it may have arisen to increase olfactory discriminatory power (46). In this view, sequence variation between alleles could give rise to sensory neurons with new odor specificities. Such variation could only be utilized through the expression of each allele individually. Alternatively, monoallelic expression may be critical to singular OR choice (12). If the choice of a receptor cluster was deterministic, while the selection of receptors from within the locus was random, then the activation of both alleles of a locus would frequently result in the expression of two different ORs in the same cell. OR regulation would therefore be dependent on the inactivation of one of the two OR loci. However, the recapitulation of OR expression by small transgenes suggests that selection occurs independent of the cluster. It is perhaps more accurate to view OR choice as stochastic. Such a process will more likely pick individual alleles, than randomly choose two copies of the same receptor. This leads to the consideration of monoallelism as a consequence and not a requirement of singular gene choice. If this is true, then the asymmetry between OR alleles, observed as an asynchrony of replication timing in fibroblasts (13), needs consideration. The observation that an OR can switch to its other allele at the same frequency with which it is initially chosen (39), suggests that OR alleles are equivalent with respect to the selection process. Thus, it is possible that the asymmetry of OR alleles is important for some biological process unrelated to OR selection.

	FUTURE DIRECTIONS

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 
The goal of future experimentation will be to determine the mechanism of the stochastic process that initially selects single OR alleles. Biochemical approaches, with in vivo validation, could be useful to identify core promoter elements in OR genes and isolate the regulatory factors that bind and activate them. It will then be possible to determine whether this transcriptional apparatus forms the core of the selection machinery and is limiting in some manner, or is abundant and gains access to only one or a few OR genes at a time. Genetic experiments designed to test the transcriptional permissiveness of OR loci could provide useful insights into the process. The similarities between OR gene choice and the regulation of antigen receptor genes may grow even more evident in the future. In parallel with observations made in lymphocytes (47), it will be interesting to examine whether chromosome dynamics and subnuclear localization may play a role in monoallelic OR expression. Neurons and lymphocytes may possibly be sharing a common stochastic mechanism to select single genes.

	ACKNOWLEDGEMENTS

 
The author wishes to thank T. Cutforth, G. Barnea, K. Baldwin, B. Datta and L. Konopasek for critical reading of the manuscript, A. Fleischmann for helpful discussions and R. Axel for helpful discussions, critical reading of the manuscript and support through a grant from the NIC/NIH No. 2 P01 CA023767.

	REFERENCES

TOP ABSTRACT INTRODUCTION EMERGENCE OF A REGULATORY... MODELS OF OR GENE... STOCHASTIC PROCESSES MAINTENANCE OF OR CHOICE PERSPECTIVES ON MONOALLELISM FUTURE DIRECTIONS REFERENCES

 

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