Research article

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

Cletus A D'Souza^1* , Vikramjit Chopra^1* , Richard Varhol¹ , Yuan-Yun Xie² , Slavita Bohacec² , Yongjun Zhao¹ , Lisa LC Lee² , Mikhail Bilenky¹ , Elodie Portales-Casamar² , An He¹ , Wyeth W Wasserman² , Daniel Goldowitz² , Marco A Marra¹ , Robert A Holt² , Elizabeth M Simpson² and Steven JM Jones¹

¹  Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave – Suite 100, Vancouver, BC, V5Z 4E6, Canada

²  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

author email corresponding author email* Contributed equally

BMC Neuroscience 2008, 9:66doi:10.1186/1471-2202-9-66

Published:	14 July 2008

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.