Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

Abstract Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with over 850 in human and nearly 1500 genes in mouse. The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons

10.1101/774612 ◽

2019 ◽

Author(s):

If H. A. Barnes ◽

Ximena Ibarra-Soria ◽

Stephen Fitzgerald ◽

Jose M. Gonzalez ◽

Claire Davidson ◽

...

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Gene Repertoire ◽

Coding Region ◽

Protein Coding ◽

Coding Sequences ◽

Coding Regions ◽

Or Gene ◽

Or Genes ◽

Human And Mouse

ABSTRACTOlfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with over 850 in human and nearly 1500 genes in mouse. The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons

10.21203/rs.2.17248/v2 ◽

2020 ◽

Author(s):

If Barnes ◽

Ximena Ibarra-Soria ◽

Stephen Fitzgerald ◽

Jose Gonzalez ◽

Claire Davidson ◽

...

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Gene Repertoire ◽

Coding Region ◽

Protein Coding ◽

Coding Sequences ◽

Coding Regions ◽

Or Gene ◽

Or Genes ◽

Human And Mouse

Abstract Background: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Results: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.Conclusions: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons

10.21203/rs.2.17248/v3 ◽

2020 ◽

Author(s):

If Habib Ahmed Barnes ◽

Ximena Ibarra-Soria ◽

Stephen Fitzgerald ◽

Jose Manuel Gonzalez ◽

Claire Davidson ◽

...

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Gene Repertoire ◽

Coding Region ◽

Protein Coding ◽

Coding Sequences ◽

Coding Regions ◽

Or Gene ◽

Or Genes ◽

Human And Mouse

Abstract Background: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Results: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.Conclusions: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

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Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons.

10.21203/rs.2.17248/v4 ◽

2020 ◽

Author(s):

If Habib Ahmed Barnes ◽

Ximena Ibarra-Soria ◽

Stephen Fitzgerald ◽

Jose Manuel Gonzalez ◽

Claire Davidson ◽

...

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Gene Repertoire ◽

Coding Region ◽

Protein Coding ◽

Coding Sequences ◽

Coding Regions ◽

Or Gene ◽

Or Genes ◽

Human And Mouse

Abstract Background Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Results Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon. Conclusions This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

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Faculty Opinions recommendation of The olfactory receptor gene superfamily of the mouse.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1004627.52854 ◽

2002 ◽

Author(s):

Peter Mombaerts

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Olfactory Receptor Gene

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Olfactory receptor gene repertoires in mammals

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis ◽

10.1016/j.mrfmmm.2006.11.012 ◽

2007 ◽

Vol 616 (1-2) ◽

pp. 95-102 ◽

Cited By ~ 38

Author(s):

Sylvie Rouquier ◽

Dominique Giorgi

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Olfactory Receptor Gene

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Differing from diseased stage in melanoma, the olfactory receptor gene OR56A4 is expressed

10.31219/osf.io/yz37x ◽

2021 ◽

Author(s):

Bronte Morse ◽

Kobi Decker

Keyword(s):

Breast Cancer ◽

Cancer Patients ◽

Olfactory Receptor ◽

Receptor Gene ◽

Stage I ◽

Stage Ii ◽

Stage Iii ◽

Olfactory Receptor Gene ◽

Breast Cancer Patients ◽

Receptor Family

We have compared the global profiles of 100 tumors in Stage I, II and III with two independently releasedmicroarray datasets in order to understand their transcriptional behaviors accompanying a progression in breastcancer (1, 2). The olfactive receptor, family 56, subfamily A, member 4 OR56A4, was discovered to have beenone of the genes with the most varied expression when comparing initial tumors in stage I, stage II, and stageIII of breast cancer patients. In the stage III tumors, OR56A4 expression in comparison to the stage I tumorswas lower.

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