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Citation for Study 19579

Citation title: "The human olfactory transcriptome".

Study name: "The human olfactory transcriptome".

This study is part of submission 19579 (Status: Published).

Citation

Olender T., Keydar I., Pinto J.M., Tatarskyy P., Fishilevich S., Alkelai A., Chien M., Restrepo D., Matsunami H., Gilad Y., & Lancet D. 2016. The human olfactory transcriptome. BMC genomics, .

Authors

• Olender T. (submitter) 972-545504539
• Keydar I.
• Pinto J.M.
• Tatarskyy P.
• Fishilevich S.
• Alkelai A.
• Chien M.
• Restrepo D.
• Matsunami H.
• Gilad Y.
• Lancet D.

Abstract

Background. Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. Results. We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs. controls. The highest overexpression is seen for lipocalins and bactericidal/permeability-increasing (BPI)-fold proteins, which in other species include secreted odorant carriers. Mouse-human discordance in orthologous lipocalin expression suggests different mammalian evolutionary paths in this family. Of the overexpressed genes 36 have documented olfactory function while for 158 there is little or no previous such functional evidence. The latter group includes GPCRs, neuropeptides, solute carriers, transcription factors and biotransformation enzymes. Many of them may be indirectly implicated in sensory function, and ~70% are over expressed also in mouse olfactory epithelium, corroborating their olfactory role. Nearly 90% of the intact OR repertoire, and ~60% of the OR pseudogenes are expressed in the olfactory epithelium, with the latter showing a 3-fold lower expression. ORs transcription levels show a 1000-fold inter-paralog variation, as well as significant inter-individual differences. We assembled 160 transcripts representing 100 intact OR genes. These include 1-4 short 5? non-coding exons with considerable alternative splicing and long last exons that contain the coding region and 3? untranslated region of highly variable length. Notably, we identified 10 ORs with an intact open reading frame but with seemingly non-functional transcripts, suggesting a yet unreported OR pseudogenization mechanism. Analysis of the OR upstream regions indicated an enrichment of the homeobox family transcription factor binding sites and a consensus localization of a specific transcription factor binding site subfamily (Olf/EBF). Conclusions. We provide an overview of expression levels of ORs and auxiliary genes in human olfactory epithelium. This forms a transcriptomic view of the entire OR repertoire, and reveals a large number of over-expressed uncharacterized human non-receptor genes, providing a platform for future discovery.

Keywords

olfaction, RNAseq, olfactory epithelium, olfactory receptor

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19579
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref26109,
  	 author = {Tsviya  Olender and Ifat   Keydar and Jayant M Pinto and Pavlo   Tatarskyy and Simon  Fishilevich and Anna  Alkelai and Ming-Shan   Chien and Diego   Restrepo and Hiroaki   Matsunami and Yoav  Gilad and Doron  Lancet},
  	 title = {The human olfactory transcriptome},
  	 year = {2016},
  	 keywords = {olfaction, RNAseq, olfactory epithelium, olfactory receptor},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC genomics},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background. Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. 
  Results. We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs. controls. The highest overexpression is seen for lipocalins and bactericidal/permeability-increasing (BPI)-fold proteins, which in other species include secreted odorant carriers. Mouse-human discordance in orthologous lipocalin expression suggests different mammalian evolutionary paths in this family. 
  Of the overexpressed genes 36 have documented olfactory function while for 158 there is little or no previous such functional evidence. The latter group includes GPCRs, neuropeptides, solute carriers, transcription factors and biotransformation enzymes. Many of them may be indirectly implicated in sensory function, and ~70% are over expressed also in mouse olfactory epithelium, corroborating their olfactory role. 
  Nearly 90% of the intact OR repertoire, and ~60% of the OR pseudogenes are expressed in the olfactory epithelium, with the latter showing a 3-fold lower expression. ORs transcription levels show a 1000-fold inter-paralog variation, as well as significant inter-individual differences. We assembled 160 transcripts representing 100 intact OR genes. These include 1-4 short 5? non-coding exons with considerable alternative splicing and long last exons that contain the coding region and 3? untranslated region of highly variable length. Notably, we identified 10 ORs with an intact open reading frame but with seemingly non-functional transcripts, suggesting a yet unreported OR pseudogenization mechanism. Analysis of the OR upstream regions indicated an enrichment of the homeobox family transcription factor binding sites and a consensus localization of a specific transcription factor binding site subfamily (Olf/EBF).
  Conclusions. We provide an overview of expression levels of ORs and auxiliary genes in human olfactory epithelium. This forms a transcriptomic view of the entire OR repertoire, and reveals a large number of over-expressed uncharacterized human non-receptor genes, providing a platform for future discovery. 
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 26109
  AU  - Olender,Tsviya 
  AU  - Keydar,Ifat  
  AU  - Pinto,Jayant M
  AU  - Tatarskyy,Pavlo  
  AU  - Fishilevich,Simon 
  AU  - Alkelai,Anna 
  AU  - Chien,Ming-Shan  
  AU  - Restrepo,Diego  
  AU  - Matsunami,Hiroaki  
  AU  - Gilad,Yoav 
  AU  - Lancet,Doron 
  T1  - The human olfactory transcriptome
  PY  - 2016
  KW  - olfaction
  KW  - RNAseq
  KW  - olfactory epithelium
  KW  - olfactory receptor
  UR  - http://dx.doi.org/
  N2  - Background. Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. 
  Results. We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs. controls. The highest overexpression is seen for lipocalins and bactericidal/permeability-increasing (BPI)-fold proteins, which in other species include secreted odorant carriers. Mouse-human discordance in orthologous lipocalin expression suggests different mammalian evolutionary paths in this family. 
  Of the overexpressed genes 36 have documented olfactory function while for 158 there is little or no previous such functional evidence. The latter group includes GPCRs, neuropeptides, solute carriers, transcription factors and biotransformation enzymes. Many of them may be indirectly implicated in sensory function, and ~70% are over expressed also in mouse olfactory epithelium, corroborating their olfactory role. 
  Nearly 90% of the intact OR repertoire, and ~60% of the OR pseudogenes are expressed in the olfactory epithelium, with the latter showing a 3-fold lower expression. ORs transcription levels show a 1000-fold inter-paralog variation, as well as significant inter-individual differences. We assembled 160 transcripts representing 100 intact OR genes. These include 1-4 short 5? non-coding exons with considerable alternative splicing and long last exons that contain the coding region and 3? untranslated region of highly variable length. Notably, we identified 10 ORs with an intact open reading frame but with seemingly non-functional transcripts, suggesting a yet unreported OR pseudogenization mechanism. Analysis of the OR upstream regions indicated an enrichment of the homeobox family transcription factor binding sites and a consensus localization of a specific transcription factor binding site subfamily (Olf/EBF).
  Conclusions. We provide an overview of expression levels of ORs and auxiliary genes in human olfactory epithelium. This forms a transcriptomic view of the entire OR repertoire, and reveals a large number of over-expressed uncharacterized human non-receptor genes, providing a platform for future discovery. 
  
  L3  - 
  JF  - BMC genomics
  VL  - 
  IS  - 
  ER  -