Transcriptomes of Mouse Olfactory Epithelium Reveal Sexual Differences in Odorant Detection

Genomics Research Center, Academia Sinica, Taipei, Taiwan, ROC.
Genome Biology and Evolution (Impact Factor: 4.23). 04/2012; 4(5):703-12. DOI: 10.1093/gbe/evs039
Source: PubMed


To sense numerous odorants and chemicals, animals have evolved a large number of olfactory receptor genes (Olfrs) in their genome. In particular, the house mouse has ~1,100 genes in the Olfr gene family. This makes the mouse a good model organism to study Olfr genes and olfaction-related genes. To date, whether male and female mice possess the same ability in detecting environmental odorants is still unknown. Using the next generation sequencing technology (paired-end mRNA-seq), we detected 1,088 expressed Olfr genes in both male and female olfactory epithelium. We found that not only Olfr genes but also odorant-binding protein (Obp) genes have evolved rapidly in the mouse lineage. Interestingly, Olfr genes tend to express at a higher level in males than in females, whereas the Obp genes clustered on the X chromosome show the opposite trend. These observations may imply a more efficient odorant-transporting system in females, whereas a more active Olfr gene expressing system in males. In addition, we detected the expression of two genes encoding major urinary proteins, which have been proposed to bind and transport pheromones or act as pheromones in mouse urine. This observation suggests a role of main olfactory system (MOS) in pheromone detection, contrary to the view that only accessory olfactory system (AOS) is involved in pheromone detection. This study suggests the sexual differences in detecting environmental odorants in MOS and demonstrates that mRNA-seq provides a powerful tool for detecting genes with low expression levels and with high sequence similarities.

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    • ". ) . Regarding FACS - sorted ORNs , we detected the expression of 582 ( homozygous ) and 905 ( heterozygous ) OR genes with FPKM > 0 . 5 . For a typical 1 kb OR coding sequence at a FPKM of 0 . 1 , the expression was confirmed by 3 reads in the OE , and due to the lower sequencing depths for FACS - sorted ORNs at a FPKM of 0 . 5 ( S3 Fig . ) . As Shiao et al . ( 2012 ) , we set a simi - lar threshold for the detection of ORs [ 51 ] . If very weakly expressed OR genes , whose expression was only supported by 1 – 2 fragments , were included , expression of an additional ~2% of ORs was detected in both male and female OEs . A total of 98 and 18 ORs had no detectable expression in male and female OEs , "
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    ABSTRACT: The ability of animals to sense and differentiate among thousands of odorants relies on a large set of olfactory receptors (OR) and a multitude of accessory proteins within the olfacto-ry epithelium (OE). ORs and related signaling mechanisms have been the subject of inten-sive studies over the past years, but our knowledge regarding olfactory processing remains limited. The recent development of next generation sequencing (NGS) techniques encour-aged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of fe-male and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice. The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome. In OE samples, nearly all OR and trace amine-associated receptor (TAAR) genes involved in the perception of volatile amines were detectably expressed. Other genes known to participate in olfactory signaling pathways were among the 200 genes with the highest expression lev-els in the OE. To identify OE-specific genes, we compared olfactory neuron expression pro-files with RNA-Seq transcriptome data from different murine tissues. By analyzing different transcript classes, we detected the expression of non-olfactory GPCRs in ORNs and established an expression ranking for GPCRs detected in the OE. We also identified other previously undescribed membrane proteins as potential new players in olfaction. The quantitative and comprehensive transcriptome data provide a virtually complete cata-logue of genes expressed in the OE and present a useful tool to uncover candidate genes involved in, for example, olfactory signaling, OR trafficking and recycling, and proliferation.
    PLoS ONE 01/2015; 10(1). DOI:10.1371/journal.pone.0113170 · 3.23 Impact Factor
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    • "Sex-biased genes identified in this study (Shiao et al. 2012) and in Kopp et al. (2008) and overlap between two studies. FC, fold changes of fragments per kilobase of exon per million fragments mapped (FPKM) values and qRT-PCR results between females (F) and males (M); FDR, false discovery rate; NA 1 , fold change was too small based on sequencing results, and we therefore did not design probes for the qRT-PCR analysis; NA 2 , not detected by Kopp et al. "
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    ABSTRACT: Antennae of fruit flies are the major organs responsible for detecting environmental volatiles, e.g., egg-laying substrates. An adult antenna contains many sensilla full of olfactory sensory neurons, where olfactory receptor (Or) genes are expressed. Each sensory neuron only expresses up to three receptors, making it difficult to estimate expression levels by conventional methods. In this study, we applied Illumina RNA sequencing (RNA-seq) to study the expression levels of Or and other genes in fly antennae. RNA from approximately 1,200 pairs of adult antennae from each sex of Drosophila melanogaster was used to obtain the antennal transcriptome of each sex. We detected approximately 12,000 genes expressed in antennae of either sex. The most highly expressed genes included pheromone-binding genes, transmembrane transporter genes, and sensory reception genes. Among the 61 annotated Or genes, we observed 53 and 54 genes (approximately 90%) expressed (fragments per kilobase of exon per million fragments mapped (FPKM) > 0.05) in male and female antennae, respectively; approximately 25 genes were expressed with FPKM > 15. Compared to previous studies, which extracted RNA from the whole body or head and used microarrays, antenna-specific transcriptomes obtained by RNA-seq provided more reliable estimates of gene expression levels and revealed many lowly expressed genes. Ninty-one genes, including one odorant-binding protein (Obp) gene and four Or genes, were differentially expressed between male and female antennae. These sexually biased genes were enriched on the X chromosome and showed enrichment in different gene ontology categories for male and female flies. The present and previous data together suggest that a gene family with putative immune response functions is related to pheromone detection and involved in the courtship behavior of male flies. Tissue-specific RNA-seq is powerful for detecting lowly expressed genes. Our study provides new insight into the expression of olfactory-related genes in Drosophila antennae.
    Zoological studies 11/2013; 52(1):42. DOI:10.1186/1810-522X-52-42 · 0.78 Impact Factor
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    ABSTRACT: Olfactory receptors (ORs) provide the molecular basis for the detection of volatile odorant molecules by olfactory sensory neurons. The OR supergene family encodes G-protein coupled proteins that belong to the seven-transmembrane-domain receptor family. It was initially postulated that ORs are exclusively expressed in the olfactory epithelium. However, recent studies have demonstrated ectopic expression of some ORs in a variety of other tissues. In the present study, we conducted a comprehensive expression analysis of ORs using an extended panel of human tissues. This analysis made use of recent dramatic technical developments of the so-called Next Generation Sequencing (NGS) technique, which encouraged us to use open access data for the first comprehensive RNA-Seq expression analysis of ectopically expressed ORs in multiple human tissues. We analyzed mRNA-Seq data obtained by Illumina sequencing of 16 human tissues available from Illumina Body Map project 2.0 and from an additional study of OR expression in testis. At least some ORs were expressed in all the tissues analyzed. In several tissues, we could detect broadly expressed ORs such as OR2W3 and OR51E1. We also identified ORs that showed exclusive expression in one investigated tissue, such as OR4N4 in testis. For some ORs, the coding exon was found to be part of a transcript of upstream genes. In total, 111 of 400 OR genes were expressed with an FPKM (fragments per kilobase of exon per million fragments mapped) higher than 0.1 in at least one tissue. For several ORs, mRNA expression was verified by RT-PCR. Our results support the idea that ORs are broadly expressed in a variety of tissues and provide the basis for further functional studies.
    PLoS ONE 02/2013; 8(2):e55368. DOI:10.1371/journal.pone.0055368 · 3.23 Impact Factor
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