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Identification of a set of genes showing regionally enriched expression in the mouse brain.

D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ - BMC Neurosci (2008)

Bottom Line: 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.GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology.This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave - Suite 100, Vancouver, BC, V5Z 4E6, Canada. cdsouza@bcgsc.ca

ABSTRACT

Background: 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.

Results: 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 in situ 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.

Conclusion: 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.

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Use of Laser Capture Microdissection to isolate the hippocampus dentate gyrus from an adult mouse. A) Intact coronal brain section at ~Bregma -1.35 stained with cresyl violet. B & C) dentate gyrus (DG) has been microdissected with laser. D) dentate gyrus has been isolated and captured for total RNA extraction and construction of SAGE libraries. Images were captured using a Sony DXC-390P 3-CCD color video camera attached to a Nikon Eclipse TE2000-S microscope (10× magnification). Scale bar = 100 μm. D: dorsal; V: ventral.
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Figure 1: Use of Laser Capture Microdissection to isolate the hippocampus dentate gyrus from an adult mouse. A) Intact coronal brain section at ~Bregma -1.35 stained with cresyl violet. B & C) dentate gyrus (DG) has been microdissected with laser. D) dentate gyrus has been isolated and captured for total RNA extraction and construction of SAGE libraries. Images were captured using a Sony DXC-390P 3-CCD color video camera attached to a Nikon Eclipse TE2000-S microscope (10× magnification). Scale bar = 100 μm. D: dorsal; V: ventral.

Mentions: To identify regionally enriched gene expression within the brain of the adult mouse strain C57BL/6J, we used the precision of Laser Capture Microdissection (LCM; Figure 1) [16] to isolate component tissues and construct SAGE libraries from 17 brain regions as well as the whole adult mouse brain for comparison (Methods). As shown in Table 1, these libraries have been sampled to a depth of > 100,000 tags each, a level shown to be adequate for the discovery of medium-to-high level transcripts [8]. Bioinformatics analysis of differential gene expression was performed as described in Methods. Since the majority of transcripts were detected in multiple libraries, we employed a heuristic approach to identify and rank expression patterns (outlined in Table 2). For each brain region, we ranked genes from 1–91 based on the level and pattern of expression in descending order. Expression specificity of a ranked list of 1999 SAGE-identified genes was then confirmed by examining related literature information and Allen Brain Atlas in situ hybridization data. Based on this collective information, region-specific or region-enriched genes were further considered.


Identification of a set of genes showing regionally enriched expression in the mouse brain.

D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ - BMC Neurosci (2008)

Use of Laser Capture Microdissection to isolate the hippocampus dentate gyrus from an adult mouse. A) Intact coronal brain section at ~Bregma -1.35 stained with cresyl violet. B & C) dentate gyrus (DG) has been microdissected with laser. D) dentate gyrus has been isolated and captured for total RNA extraction and construction of SAGE libraries. Images were captured using a Sony DXC-390P 3-CCD color video camera attached to a Nikon Eclipse TE2000-S microscope (10× magnification). Scale bar = 100 μm. D: dorsal; V: ventral.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483290&req=5

Figure 1: Use of Laser Capture Microdissection to isolate the hippocampus dentate gyrus from an adult mouse. A) Intact coronal brain section at ~Bregma -1.35 stained with cresyl violet. B & C) dentate gyrus (DG) has been microdissected with laser. D) dentate gyrus has been isolated and captured for total RNA extraction and construction of SAGE libraries. Images were captured using a Sony DXC-390P 3-CCD color video camera attached to a Nikon Eclipse TE2000-S microscope (10× magnification). Scale bar = 100 μm. D: dorsal; V: ventral.
Mentions: To identify regionally enriched gene expression within the brain of the adult mouse strain C57BL/6J, we used the precision of Laser Capture Microdissection (LCM; Figure 1) [16] to isolate component tissues and construct SAGE libraries from 17 brain regions as well as the whole adult mouse brain for comparison (Methods). As shown in Table 1, these libraries have been sampled to a depth of > 100,000 tags each, a level shown to be adequate for the discovery of medium-to-high level transcripts [8]. Bioinformatics analysis of differential gene expression was performed as described in Methods. Since the majority of transcripts were detected in multiple libraries, we employed a heuristic approach to identify and rank expression patterns (outlined in Table 2). For each brain region, we ranked genes from 1–91 based on the level and pattern of expression in descending order. Expression specificity of a ranked list of 1999 SAGE-identified genes was then confirmed by examining related literature information and Allen Brain Atlas in situ hybridization data. Based on this collective information, region-specific or region-enriched genes were further considered.

Bottom Line: 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.GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology.This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave - Suite 100, Vancouver, BC, V5Z 4E6, Canada. cdsouza@bcgsc.ca

ABSTRACT

Background: 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.

Results: 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 in situ 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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus