NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

LINE-1 specific nuclear organization in mice olfactory sensory neurons

Long interspersed nuclear elements-1 (LINE-1) are mobile DNA elements that comprise the majority of interspersed repeats in the mammalian genome. During the last decade, these transposable sequences have been described as controlling elements involved in transcriptional regulation and genome plasticity. Recently, LINE-1 have been implicated in neurogenesis, but to date little is known about their nuclear organization in neurons. The olfactory epithelium is a site of continuous neurogenesis, and loci of olfactory receptor genes are enriched in LINE-1 copies. Olfactory neurons have a unique inverted nuclear architecture and constitutive heterochromatin forms a block in the center of the nuclei. Our DNA FISH images show that, even though LINE-1 copies are dispersed throughout the mice genome, they are clustered forming a cap around the central heterochromatin block and frequently occupy the same position as facultative heterochromatin in olfactory neurons nuclei. This specific LINE-1 organization could not be observed in other olfactory epithelium cell types. Analyses of H3K27me3 and H3K9me3 ChIP-seq data from olfactory epithelium revealed that LINE-1 copies located at OR gene loci show different enrichment for these heterochromatin marks. We also found that LINE-1 are transcribed in mouse olfactory epithelium. These results suggest that LINE-1 play a role in the olfactory neurons' nuclear architecture. SIGNIFICANCE STATEMENT: LINE-1 are mobile DNA elements and comprise almost 20% of mice and human genomes. These retrotransposons have been implicated in neurogenesis. We show for the first time that LINE-1 retrotransposons have a specific nuclear organization in olfactory neurons, forming aggregates concentric to the heterochromatin block and frequently occupying the same region as facultative heterochromatin. We found that LINE-1 at olfactory receptor gene loci are differently enriched for H3K9me3 and H3K27me3, but LINE-1 transcripts could be detected in the olfactory epithelium. We speculate that these retrotransposons play an active role in olfactory neurons' nuclear architecture.

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner

Minisatellites, also called variable number of tandem repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Their identification and role as expression quantitative trait loci (eQTL) have been limited by their absence in comparative genomic hybridization and single nucleotide polymorphisms arrays. By taking advantage of cap analysis of gene expression (CAGE), we describe a new example of a minisatellite hosting a transcription start site (TSS) which expression is dependent on the repeat number. It is located in the third intron of the gene nitrogen permease regulator like protein 3 (NPRL3). NPRL3 is a component of the GAP activity toward rags 1 protein complex that inhibits mammalian target of rapamycin complex 1 (mTORC1) activity and it is found mutated in familial focal cortical dysplasia and familial focal epilepsy. CAGE tags represent an alternative TSS identifying TAGNPRL3 messenger RNAs (mRNAs). TAGNPRL3 is expressed in red blood cells both at mRNA and protein levels, it interacts with its protein partner NPRL2 and its overexpression inhibits cell proliferation. This study provides an example of a minisatellite that is both a TSS and an eQTL as well as identifies a new VNTR that may modify mTORC1 activity.

Expression of homeobox genes in the mouse olfactory epithelium

Homeobox genes constitute a large family of genes widely studied because of their role in the establishment of the body pattern. However, they are also involved in many other events during development and adulthood. The main olfactory epithelium (MOE) is an excellent model to study neurogenesis in the adult nervous system. Analyses of homeobox genes during development show that some of these genes are involved in the formation and establishment of cell diversity in the MOE. Moreover, the mechanisms of expression of odorant receptors (ORs) constitute one of the biggest enigmas in the field. Analyses of OR promoters revealed the presence of homeodomain binding sites in their sequences. Here we characterize the expression patterns of a set of 49 homeobox genes in the MOE with in situ hybridization. We found that seven of them (Dlx3, Dlx5, Dlx6, Msx1, Meis1, Isl1, and Pitx1) are zonally expressed. The homeobox gene Emx1 is expressed in three guanylate cyclase(+) populations, two located in the MOE and the third one in an olfactory subsystem known as Grüneberg ganglion located at the entrance of the nasal cavity. The homeobox gene Tshz1 is expressed in a unique patchy pattern across the MOE. Our findings provide new insights to guide functional studies that aim to understand the complexity of transcription factor expression and gene regulation in the MOE. J. Comp. Neurol. 524:2713-2739, 2016. © 2016 Wiley Periodicals, Inc.

CD36 is expressed in a defined subpopulation of neurons in the olfactory epithelium

The sensory neurons in the olfactory epithelium (OSNs) are equipped with a large repertoire of olfactory receptors and the associated signal transduction machinery. In addition to the canonical OSNs, which express odorant receptors (ORs), the epithelium contains specialized subpopulations of sensory neurons that can detect specific information from environmental cues and relay it to relevant neuronal circuitries. Here we describe a subpopulation of mature OSNs in the main olfactory epithelium (MOE) which expresses CD36, a multifunctional receptor involved in a series of biological processes, including sensory perception of lipid ligands. The Cd36 expressing neurons coexpress markers of mature OSNs and are dispersed throughout the MOE. Unlike several ORs analyzed in our study, we found frequent coexpression of the OR Olfr287 in these neurons, suggesting that only a specific set of ORs may be coexpressed with CD36 in OSNs. We also show that CD36 is expressed in the cilia of OSNs, indicating a possible role in odorant detection. CD36-deficient mice display no signs of gross changes in the organization of the olfactory epithelium, but show impaired preference for a lipid mixture odor. Our results show that CD36-expressing neurons represent a distinct population of OSNs, which may have specific functions in olfaction.

Laser capture microdissection: Big data from small samples

Any tissue is made up of a heterogeneous mix of spatially distributed cell types. In response to any (patho) physiological cue, responses of each cell type in any given tissue may be unique and cannot be homogenized across cell-types and spatial co-ordinates. For example, in response to myocardial infarction, on one hand myocytes and fibroblasts of the heart tissue respond differently. On the other hand, myocytes in the infarct core respond differently compared to those in the peri-infarct zone. Therefore, isolation of pure targeted cells is an important and essential step for the molecular analysis of cells involved in the progression of disease. Laser capture microdissection (LCM) is powerful to obtain a pure targeted cell subgroup, or even a single cell, quickly and precisely under the microscope, successfully tackling the problem of tissue heterogeneity in molecular analysis. This review presents an overview of LCM technology, the principles, advantages and limitations and its down-stream applications in the fields of proteomics, genomics and transcriptomics. With powerful technologies and appropriate applications, this technique provides unprecedented insights into cell biology from cells grown in their natural tissue habitat as opposed to those cultured in artificial petri dish conditions.

Mammalian pheromones: emerging properties and mechanisms of detection

The concept of mammalian pheromones was established decades before the discovery of any bioactive ligands. Therefore, their molecular identity, native sources, and the meaning of their detection has been largely speculative. There has been recent success in identifying a variety of candidate mouse pheromones and other specialized odors. These discoveries reveal that mammalian pheromones come in a variety of ligand types and they are detected by sensory neurons that are pre-set to promote an array of social and survival behaviors. Importantly, recent findings show that they activate molecularly diverse sensory neurons that differ from canonical odorant detectors. These novel sensory neurons hold future promise to unlock the mystery of how their detection is hardwired to generate behavior.

Functional promiscuity in a mammalian chemosensory system: extensive expression of vomeronasal receptors in the main olfactory epithelium of mouse lemurs

The vomeronasal organ (VNO) is functional in most terrestrial mammals, though progressively reduced in the primate lineage, and is used for intraspecific communication and predator recognition. Vomeronasal receptor (VR) genes comprise two families of chemosensory genes (V1R and V2R) that have been considered to be specific for the VNO. However, recently a large number of VRs were reported to be expressed in the main olfactory epithelium (MOE) of mice, but there is little knowledge of the expression of these genes outside of rodents. To explore the function of VR genes in mammalian evolution, we analyzed and compared the expression of 64 V1R and 2 V2R genes in the VNO and the MOE of the gray mouse lemur (Microcebus murinus), the primate with the largest known VR repertoire. We furthermore compared expression patterns in adults of both sexes and seasons, and in an infant. A large proportion (83-97%) of the VR loci was expressed in the VNO of all individuals. The repertoire in the infant was as rich as in adults, indicating reliance on olfactory communication from early postnatal development onwards. In concordance with mice, we also detected extensive expression of VRs in the MOE, with proportions of expressed loci in individuals ranging from 29 to 45%. TRPC2, which encodes a channel protein crucial for signal transduction via VRs, was co-expressed in the MOE in all individuals indicating likely functionality of expressed VR genes in the MOE. In summary, the large VR repertoire in mouse lemurs seems to be highly functional. Given the differences in the neural pathways of MOE and VNO signals, which project to higher cortical brain centers or the limbic system, respectively, this raises the intriguing possibility that the evolution of MOE-expression of VRs enabled mouse lemurs to adaptively diversify the processing of VR-encoded olfactory information.

Trpc2-expressing sensory neurons in the main olfactory epithelium of the mouse

The mouse olfactory system contains two distinct chemosensory epithelia, the main olfactory epithelium (MOE) and the vomeronasal epithelium (VNE). Their sensory neurons express odorant receptor genes and vomeronasal receptor genes, respectively, and differ fundamentally in their signal transduction pathways. Genes required for chemosensory transduction are the cyclic nucleotide-gated channel subunit Cnga2 and the transient receptor potential cation channel Trpc2, respectively. Here, we document two previously unrecognized types of Trpc2+ neurons in the MOE of mice of various ages, including adults. These cell types express Cnga2 and can be distinguished by expression of adenylate cyclase Adcy3 (positive: type A; negative: type B). A third of MOE neurons that express the odorant receptor genes Olfr68/Olfr69 coexpress Trpc2 and are type A cells. In Trpc2-IRES-taulacZ gene-targeted mice, some labeled axons coalesce into glomeruli in the main olfactory bulb. Our findings have implications for the conventional VNE-centric interpretation of the behavioral phenotypes of Trpc2 knockout mice.