Identification of a set of genes showing regionally enriched expression in the mouse brain
Identifieur interne : 002181 ( Main/Exploration ); précédent : 002180; suivant : 002182Identification of a set of genes showing regionally enriched expression in the mouse brain
Auteurs : Cletus A. D'Souza [Canada] ; Vikramjit Chopra [Canada] ; Richard Varhol [Canada] ; Yuan-Yun Xie [Canada] ; Slavita Bohacec [Canada] ; Yongjun Zhao [Canada] ; Lisa Lc Lee [Canada] ; Mikhail Bilenky [Canada] ; Elodie Portales-Casamar [Canada] ; An He [Canada] ; Wyeth W. Wasserman [Canada] ; Daniel Goldowitz [Canada] ; Marco A. Marra [Canada] ; Robert A. Holt [Canada] ; Elizabeth M. Simpson [Canada] ; Steven Jm Jones [Canada]Source :
- BMC Neuroscience [ 1471-2202 ] ; 2008.
Abstract
The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain.
We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas
Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.
Url:
DOI: 10.1186/1471-2202-9-66
PubMed: 18625066
PubMed Central: 2483290
Affiliations:
Links toward previous steps (curation, corpus...)
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- to stream Ncbi, to step Curation: 000935
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Le document en format XML
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4H4</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Yongjun" sort="Zhao, Yongjun" uniqKey="Zhao Y" first="Yongjun" last="Zhao">Yongjun Zhao</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Lisa Lc" sort="Lee, Lisa Lc" uniqKey="Lee L" first="Lisa Lc" last="Lee">Lisa Lc Lee</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Bilenky, Mikhail" sort="Bilenky, Mikhail" uniqKey="Bilenky M" first="Mikhail" last="Bilenky">Mikhail Bilenky</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Portales Casamar, Elodie" sort="Portales Casamar, Elodie" uniqKey="Portales Casamar E" first="Elodie" last="Portales-Casamar">Elodie Portales-Casamar</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="He, An" sort="He, An" uniqKey="He A" first="An" last="He">An He</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. 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D'Souza</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Chopra, Vikramjit" sort="Chopra, Vikramjit" uniqKey="Chopra V" first="Vikramjit" last="Chopra">Vikramjit Chopra</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Varhol, Richard" sort="Varhol, Richard" uniqKey="Varhol R" first="Richard" last="Varhol">Richard Varhol</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Xie, Yuan Yun" sort="Xie, Yuan Yun" uniqKey="Xie Y" first="Yuan-Yun" last="Xie">Yuan-Yun Xie</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Bohacec, Slavita" sort="Bohacec, Slavita" uniqKey="Bohacec S" first="Slavita" last="Bohacec">Slavita Bohacec</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Yongjun" sort="Zhao, Yongjun" uniqKey="Zhao Y" first="Yongjun" last="Zhao">Yongjun Zhao</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Lee, Lisa Lc" sort="Lee, Lisa Lc" uniqKey="Lee L" first="Lisa Lc" last="Lee">Lisa Lc Lee</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Bilenky, Mikhail" sort="Bilenky, Mikhail" uniqKey="Bilenky M" first="Mikhail" last="Bilenky">Mikhail Bilenky</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Portales Casamar, Elodie" sort="Portales Casamar, Elodie" uniqKey="Portales Casamar E" first="Elodie" last="Portales-Casamar">Elodie Portales-Casamar</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="He, An" sort="He, An" uniqKey="He A" first="An" last="He">An He</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. Wasserman</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Goldowitz, Daniel" sort="Goldowitz, Daniel" uniqKey="Goldowitz D" first="Daniel" last="Goldowitz">Daniel Goldowitz</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Holt, Robert A" sort="Holt, Robert A" uniqKey="Holt R" first="Robert A" last="Holt">Robert A. Holt</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Simpson, Elizabeth M" sort="Simpson, Elizabeth M" uniqKey="Simpson E" first="Elizabeth M" last="Simpson">Elizabeth M. Simpson</name><affiliation wicri:level="1"><nlm:aff id="I2">Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., Vancouver, BC, V5Z 4H4</wicri:regionArea><wicri:noRegion>V5Z 4H4</wicri:noRegion></affiliation></author><author><name sortKey="Jones, Steven Jm" sort="Jones, Steven Jm" uniqKey="Jones S" first="Steven Jm" last="Jones">Steven Jm Jones</name><affiliation wicri:level="1"><nlm:aff id="I1">Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6</wicri:regionArea><wicri:noRegion>V5Z 4E6</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Neuroscience</title><idno type="eISSN">1471-2202</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain.</p></sec><sec><title>Results</title><p>We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas <italic>in situ </italic>hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology.</p></sec><sec><title>Conclusion</title><p>Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="D Souza, Cletus A" sort="D Souza, Cletus A" uniqKey="D Souza C" first="Cletus A" last="D'Souza">Cletus A. D'Souza</name></noRegion><name sortKey="Bilenky, Mikhail" sort="Bilenky, Mikhail" uniqKey="Bilenky M" first="Mikhail" last="Bilenky">Mikhail Bilenky</name><name sortKey="Bohacec, Slavita" sort="Bohacec, Slavita" uniqKey="Bohacec S" first="Slavita" last="Bohacec">Slavita Bohacec</name><name sortKey="Chopra, Vikramjit" sort="Chopra, Vikramjit" uniqKey="Chopra V" first="Vikramjit" last="Chopra">Vikramjit Chopra</name><name sortKey="Goldowitz, Daniel" sort="Goldowitz, Daniel" uniqKey="Goldowitz D" first="Daniel" last="Goldowitz">Daniel Goldowitz</name><name sortKey="He, An" sort="He, An" uniqKey="He A" first="An" last="He">An He</name><name sortKey="Holt, Robert A" sort="Holt, Robert A" uniqKey="Holt R" first="Robert A" last="Holt">Robert A. Holt</name><name sortKey="Jones, Steven Jm" sort="Jones, Steven Jm" uniqKey="Jones S" first="Steven Jm" last="Jones">Steven Jm Jones</name><name sortKey="Lee, Lisa Lc" sort="Lee, Lisa Lc" uniqKey="Lee L" first="Lisa Lc" last="Lee">Lisa Lc Lee</name><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name><name sortKey="Portales Casamar, Elodie" sort="Portales Casamar, Elodie" uniqKey="Portales Casamar E" first="Elodie" last="Portales-Casamar">Elodie Portales-Casamar</name><name sortKey="Simpson, Elizabeth M" sort="Simpson, Elizabeth M" uniqKey="Simpson E" first="Elizabeth M" last="Simpson">Elizabeth M. Simpson</name><name sortKey="Varhol, Richard" sort="Varhol, Richard" uniqKey="Varhol R" first="Richard" last="Varhol">Richard Varhol</name><name sortKey="Wasserman, Wyeth W" sort="Wasserman, Wyeth W" uniqKey="Wasserman W" first="Wyeth W" last="Wasserman">Wyeth W. Wasserman</name><name sortKey="Xie, Yuan Yun" sort="Xie, Yuan Yun" uniqKey="Xie Y" first="Yuan-Yun" last="Xie">Yuan-Yun Xie</name><name sortKey="Zhao, Yongjun" sort="Zhao, Yongjun" uniqKey="Zhao Y" first="Yongjun" last="Zhao">Yongjun Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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