Monogenic and Monoallelic Expression of Odorant Receptors

Olfactory Development and Dysfunction: Involvement of Microglia

Olfactory deficits are increasingly recognized in a variety of neurological, neurodevelopmental, psychiatric, and viral diseases. While the pathology underlying olfactory loss is likely to differ across diseases, one shared feature may be an immune response mediated by microglia. Microglia orchestrate the brain's response to environmental insults and maintain neurodevelopmental homeostasis. Here, we explore the potential involvement of microglia in olfactory development and loss in disease. The effects of microglia-mediated immune response during development may be of special relevance to the olfactory system, which is unique in both its vulnerability to environmental insults as well as its extended period of neurogenesis and neuronal migration.

Transformation of an olfactory placode-derived cell into one with stem cell characteristics by disrupting epigenetic barriers

The mammalian olfactory neuronal lineage is regenerative, and accordingly, maintains a population of pluripotent cells that replenish olfactory sensory neurons and other olfactory cell types during the life of the animal. Moreover, in response to acute injury, the early transit amplifying cells along the olfactory sensory neuronal lineage are able to de-differentiate to shift resources in support of tissue restoration. In order to further explore plasticity of various cellular stages along the olfactory sensory neuronal lineage, we challenged the epigenetic stability of two olfactory placode-derived cell lines that model immature olfactory sensory neuronal stages. We found that perturbation of the Ehmt2 chromatin modifier transformed the growth properties, morphology, and gene expression profiles towards states with several stem cell characteristics. This transformation was dependent on continued expression of the large T-antigen, and was enhanced by Sox2 over-expression. These findings may provide momentum for exploring inherent cellular plasticity within early cell types of the olfactory lineage, as well as potentially add to our knowledge of cellular reprogramming.

SUMMARY STATEMENT

Discovering how epigenetic modifications influence olfactory neuronal lineage plasticity offers insights into regenerative potential and cellular reprogramming.

E-cigarette Flavors, Sensory Perception, and Evoked Responses

The chemosensory experiences evoked by flavors encompass a number of unique sensations that include olfactory stimuli (smell), gustatory stimuli (taste, i.e., salty, sweet, sour, bitter, and umami (also known as "savoriness")), and chemesthesis (touch). As such, the responses evoked by flavors are complex and, as briefly stated above, involve multiple perceptive mechanisms. The practice of adding flavorings to tobacco products dates back to the 17th century but is likely much older. More recently, the electronic cigarette or "e-cigarette" and its accompanying flavored e-liquids emerged on to the global market. These new products contain no combustible tobacco but often contain large concentrations (reported from 0 to more than 50 mg/mL) of nicotine as well as numerous flavorings and/or flavor chemicals. At present, there are more than 400 e-cigarette brands available along with potentially >15,000 different/unique flavored products. However, surprisingly little is known about the flavors/flavor chemicals added to these products, which can account for >1% by weight of some e-liquids, and their resultant chemosensory experiences, and the US FDA has done relatively little, until recently, to regulate these products. This article will discuss e-cigarette flavors and flavor chemicals, their elicited responses, and their sensory effects in some detail.

Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation

Histone variants, such as histone H3.3, replace canonical histones within the nucleosome to alter chromatin accessibility and gene expression. Although the biological roles of selected histone post-translational modifications (PTMs) have been extensively characterized, the potential differences in the function of a given PTM on different histone variants is almost always elusive. By applying proteomics and genomics techniques, we investigate the role of lysine 27 tri-methylation specifically on the histone variant H3.3 (H3.3K27me3) in the context of mouse embryonic stem cell pluripotency and differentiation as a model system for development. We demonstrate that while the steady state overall levels of methylation on both H3K27 and H3.3K27 decrease during differentiation, methylation dynamics studies indicate that methylation on H3.3K27 is maintained more than on H3K27. Using a custom-made antibody, we identify a unique enrichment of H3.3K27me3 at lineage-specific genes, such as olfactory receptor genes, and at binding motifs for the transcription factors FOXJ2/3. REST, a predicted FOXJ2/3 target that acts as a transcriptional repressor of terminal neuronal genes, was identified with H3.3K27me3 at its promoter region. H3.3K27A mutant cells confirmed an upregulation of FOXJ2/3 targets upon the loss of methylation at H3.3K27. Thus, while canonical H3K27me3 has been characterized to regulate the expression of transcription factors that play a general role in differentiation, our work suggests H3.3K27me3 is essential for regulating distinct terminal differentiation genes. This work highlights the importance of understanding the effects of PTMs not only on canonical histones but also on specific histone variants, as they may exhibit distinct roles.

May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression

How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.

Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines

The mammalian olfactory system consists of sensory neurons with specialized odorant-binding capability accomplished by mutually exclusive odorant receptor (OR) expression. Mutually exclusive OR expression is a complex multi-step process regulated by a number of cis and trans factors, including pan-silencing of all OR genes preceding the robust and stable expression of the one OR selected in each sensory neuron. We transfected two olfactory-placode-derived cell lines modeling immature odorant sensory neurons, as well as the GD25 fibroblast cell line, with episomes containing CMV-driven GFP and TK-driven hygromycin reporter genes. We inserted various coding sequences, along with an IRES, immediately upstream of the GFP gene to produce bicistronic mRNAs driven from the local CMV promoter. We found that the presence of several OR coding sequences resulted in significantly diminished episomal expression of GFP in all three cell lines. These findings suggest that OR coding sequences have intrinsic self-silencing capability that might facilitate mutually exclusive OR expression in olfactory sensory neurons by making it less likely that multiple ORs acquire an above-threshold level of expression at once.

Introns control stochastic allele expression bias

Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.

Olfactory receptor-dependent receptor repression in Drosophila

In olfactory systems across phyla, most sensory neurons express a single olfactory receptor gene selected from a large genomic repertoire. We describe previously unknown receptor gene-dependent mechanisms that ensure singular expression of receptors encoded by a tandem gene array [Ionotropic receptor 75c (Ir75c), Ir75b, and Ir75a, organized 5' to 3'] in Drosophila melanogaster Transcription from upstream genes in the cluster runs through the coding region of downstream loci and inhibits their expression in cis, most likely via transcriptional interference. Moreover, Ir75c blocks accumulation of other receptor proteins in trans through a protein-dependent, posttranscriptional mechanism. These repression mechanisms operate in endogenous neurons, in conjunction with cell type-specific gene regulatory networks, to ensure unique receptor expression. Our data provide evidence for inter-olfactory receptor regulation in invertebrates and highlight unprecedented, but potentially widespread, mechanisms for ensuring exclusive expression of chemosensory receptors, and other protein families, encoded by tandemly arranged genes.

Principles of odor coding in vertebrates and artificial chemosensory systems

The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.

Genetic Background Effects on the Expression of an Odorant Receptor Gene

There are more than 1000 odorant receptor (OR) genes in the mouse genome. Each olfactory sensory neuron expresses only one of these genes, in a monoallelic fashion. The transcript abundance of homologous OR genes vary between distinct mouse strains. Here we analyzed the expression of the OR gene Olfr17 (also named P2) in different genomic contexts. Olfr17 is expressed at higher levels in the olfactory epithelium from 129 mice than from C57BL/6 (B6) mice. However, we found that in P2-IRES-tauGFP knock-in mice, the transcript levels of the 129 Olfr17 allele are highly reduced when compared to the B6 Olfr17 allele. To address the mechanisms involved in this variation we compared the 5′ region sequence and DNA methylation patterns of the B6 and 129 Olfr17 alleles. Our results show that genetic variations in cis regulatory regions can lead to differential DNA methylation frequencies in these OR gene alleles. They also show that expression of the Olfr17 alleles is largely affected by the genetic background, and suggest that in knock-in mice, expression can be affected by epigenetic modifications in the region of the targeted locus.

Odor coding in the mammalian olfactory epithelium

Noses are extremely sophisticated chemical detectors allowing animals to use scents to interpret and navigate their environments. Odor detection starts with the activation of odorant receptors (ORs), expressed in mature olfactory sensory neurons (OSNs) populating the olfactory mucosa. Different odorants, or different concentrations of the same odorant, activate unique ensembles of ORs. This mechanism of combinatorial receptor coding provided a possible explanation as to why different odorants are perceived as having distinct odors. Aided by new technologies, several recent studies have found that antagonist interactions also play an important role in the formation of the combinatorial receptor code. These findings mark the start of a new era in the study of odorant-receptor interactions and add a new level of complexity to odor coding in mammals.

The Role of Olfactory Genes in the Expression of Rodent Paternal Care Behavior

Olfaction is the dominant sensory modality in rodents, and is crucial for regulating social behaviors, including parental care. Paternal care is rare in rodents, but can have significant consequences for offspring fitness, suggesting a need to understand the factors that regulate its expression. Pup-related odor cues are critical for the onset and maintenance of paternal care. Here, I consider the role of olfaction in the expression of paternal care in rodents. The medial preoptic area shares neural projections with the olfactory and accessory olfactory bulbs, which are responsible for the interpretation of olfactory cues detected by the main olfactory and vomeronasal systems. The olfactory, trace amine, membrane-spanning 4-pass A, vomeronasal 1, vomeronasal 2 and formyl peptide receptors are all involved in olfactory detection. I highlight the roles that 10 olfactory genes play in the expression of direct paternal care behaviors, acknowledging that this list is not exhaustive. Many of these genes modulate parental aggression towards intruders, and facilitate the recognition and discrimination of pups in general. Much of our understanding comes from studies on non-naturally paternal laboratory rodents. Future studies should explore what role these genes play in the regulation and expression of paternal care in naturally biparental species.

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model

Very little is known about long non-coding RNAs (lncRNAs) in the mammalian olfactory sensory epithelia. Deciphering the non-coding transcriptome in olfaction is relevant because these RNAs have been shown to play a role in chromatin modification and nuclear architecture reorganization, processes that accompany olfactory differentiation and olfactory receptor gene choice, one of the most poorly understood gene regulatory processes in mammals. In this study, we used a combination of in silico and ex vivo approaches to uncover a comprehensive catalogue of olfactory lncRNAs and to investigate their expression in the mouse olfactory organs. Initially, we used a novel machine-learning lncRNA classifier to discover hundreds of annotated and unannotated lncRNAs, some of which were predicted to be preferentially expressed in the main olfactory epithelium and the vomeronasal organ, the most important olfactory structures in the mouse. Moreover, we used whole-tissue and single-cell RNA sequencing data to discover lncRNAs expressed in mature sensory neurons of the main epithelium. Candidate lncRNAs were further validated by in situ hybridization and RT-PCR, leading to the identification of lncRNAs found throughout the olfactory epithelia, as well as others exquisitely expressed in subsets of mature olfactory neurons or progenitor cells.

A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers

BACKGROUND

In most mammals, a vast array of genes coding for chemosensory receptors mediates olfaction. Odorant receptor (OR) genes generally constitute the largest multifamily (> 1100 intact members in the mouse). From the whole pool, each olfactory neuron expresses a single OR allele following poorly characterized mechanisms termed OR gene choice. OR genes are found in genomic aggregations known as clusters. Nearby enhancers, named elements, are crucial regulators of OR gene choice. Despite their importance, searching for new elements is burdensome. Other chemosensory receptor genes responsible for smell adhere to expression modalities resembling OR gene choice, and are arranged in genomic clusters - often with chromosomal linkage to OR genes. Still, no elements are known for them.

RESULTS

Here we present an inexpensive framework aimed at predicting elements. We redefine cluster identity by focusing on multiple receptor gene families at once, and exemplify thirty - not necessarily OR-exclusive - novel candidate enhancers.

CONCLUSIONS

The pipeline we introduce could guide future in vivo work aimed at discovering/validating new elements. In addition, our study provides an updated and comprehensive classification of all genomic loci responsible for the transduction of olfactory signals in mammals.

Genetic Depletion of Class I Odorant Receptors Impacts Perception of Carboxylic Acids

The mammalian main olfactory pathway detects myriad volatile chemicals using >1,000 odorant receptor (OR) genes, which are organized into two phylogenetically distinct classes (class I and class II). An important question is how these evolutionarily conserved classes contribute to odor perception. Here, we report functional inactivation of a large number of class I ORs in mice via identification and deletion of a local cis-acting enhancer in the class I gene cluster. This manipulation reduced expression of half of the 131 intact class I genes. The resulting class I-depleted mice exhibited a significant reduction in the number of glomeruli responding to carboxylic acids-chemicals associated with microbial action and body odors. These mice also exhibit a change in odor perception marked by a selective loss of behavioral aversion to these compounds. Together, our data demonstrate that class I ORs play a critical role in representing a class of biologically relevant chemosignals.

Olfactory receptor function

Olfaction plays a critical role in several aspects of life. Olfactory disorders are very common in the general population, and can lead to malnutrition, weight loss, food poisoning, depression, and other disturbances. Odorants are first detected in the upper region of the nose by the main olfactory epithelium (OE). In this region, millions of olfactory sensory neurons (OSNs) interact with odor molecules through the odorant receptors (ORs), which belong to the superfamily of G protein-coupled receptors. The binding of odors to the ORs initiates an electrical signal that travels along the axons to the main olfactory bulb of the brain. The information is then transmitted to other regions of the brain, leading to odorant perception and emotional and behavioral responses. In the OE, OSNs die and are continuously replaced from stem cells localized in the epithelium's basal region. Damage to this epithelium can be caused by multiple factors, leading to anosmia (smell loss). In this chapter, we introduce the basic organization of the OE and focus on the molecular mechanisms involved in odorant perception. We also describe recent experiments that address the mechanisms of OSNs regeneration in response to neuronal injury.

Combining In Vivo and In Vitro Approaches To Identify Human Odorant Receptors Responsive to Food Odorants

Olfactory perception plays an important role in food flavor. Humans have around 400 odorant receptors (ORs), which can be activated by an enormous number of odorants in a combinatorial fashion. To date, only a few odorant receptors have been linked to their respective odorants, due to the difficulties in expressing these receptor proteins in heterologous cell systems. In vivo approaches allow for the analysis of odorant-receptor interactions in their native environment and have the advantage that the complete OR repertoire is simultaneously tested. Once mouse odorant-receptor pairs are defined, one can search for the corresponding human orthologues, which can be validated against the odorants in heterologous cells. Thus, the combination of in vivo and in vitro methods should contribute to the identification of human ORs that recognize odorants of interest, such as key food odorants.

Rearrangement of Actin Microfilaments in the Development of Olfactory Receptor Cells in Fish

At present, it remains poorly understood how the olfactory neuron migrates through the thick neuroepithelium during its maturation from a stem cell and how it develops a specific sensitivity to environmental odorants after maturation. We investigated the cytochemical features associated with the development of olfactory cells before and after the incorporation of dendrites into the surface of the olfactory epithelium. Using cytochemical staining for the actin cytoskeleton and other cell components, we found that immature neurons acquire a streamlined shape that resembles a «hot-dog» during their migration: a dense layer of actin microfilaments forms beneath the surface membrane of the growing dendrite, and the bulk of the nuclear material moves inside this layer. We have found that when the cell makes contact with its environment, the dendritic terminal develops a wide actin layer, inside which a pore is formed. It is assumed that the functional receptors of odorants generate across this pore the first intracellular signal from environmental water-soluble odorants. These data illustrate the important role of the cytoskeleton in the differentiation of olfactory cells.

Functional odor classification through a medicinal chemistry approach

Crucial for any hypothesis about odor coding is the classification and prediction of sensory qualities in chemical compounds. The relationship between perceptual quality and molecular structure has occupied olfactory scientists throughout the 20th century, but details of the mechanism remain elusive. Odor molecules are typically organic compounds of low molecular weight that may be aliphatic or aromatic, may be saturated or unsaturated, and may have diverse functional polar groups. However, many molecules conforming to these characteristics are odorless. One approach recently used to solve this problem was to apply machine learning strategies to a large set of odors and human classifiers in an attempt to find common and unique chemical features that would predict a chemical's odor. We use an alternative method that relies more on the biological responses of olfactory sensory neurons and then applies the principles of medicinal chemistry, a technique widely used in drug discovery. We demonstrate the effectiveness of this strategy through a classification for esters, an important odorant for the creation of flavor in wine. Our findings indicate that computational approaches that do not account for biological responses will be plagued by both false positives and false negatives and fail to provide meaningful mechanistic data. However, the two approaches used in tandem could resolve many of the paradoxes in odor perception.

Fluorescence-Activated Cell Sorting of Olfactory Sensory Neuron Subpopulations

The mouse olfactory epithelium is composed of a heterogeneous population of olfactory sensory neurons, where each neuron expresses one single type of odorant receptor gene, out of a repertoire of ~1000 different genes. Fluorescent-activated cell sorting (FACS) is a powerful technique, which can be used to isolate a cellular subpopulation from a heterogeneous tissue. The sorted neurons can then be used in gene expression studies, or analyzed for the presence of different DNA epigenetic modification marks. Here we describe a method to separate a subpopulation of olfactory sensory neurons expressing the odorant receptor Olfr17. In this method, the main olfactory epithelium from transgenic Olfr17-IRES-GFP mice is dissociated into single cells, followed by separation of the GFP positive cells by FACS.

A Latin American Perspective on G Protein-Coupled Receptors

G protein-coupled receptors are sensors that interact with a large variety of elements, including photons, ions, and large proteins. Not surprisingly, these receptors participate in the numerous normal physiologic processes that we refer to as health and in its perturbations that constitute disease. It has been estimated that a large percentage of drugs currently used in therapeutics target these proteins, and this percentage is larger when illegal drugs are included. The state of the art in this field can be defined with the oxymoron "constant change," and enormous progress has been made in recent years. A group of scientists working in Latin America were invited to contribute minireviews for this special section to present some of the work performed in this geographical region and foster further international collaboration.