Identification of a set of genes showing regionally enriched expression in the mouse brainReport as inadecuate




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BMC Neuroscience

, 9:66

First Online: 14 July 2008Received: 24 December 2007Accepted: 14 July 2008

Abstract

BackgroundThe 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.

ResultsWe 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.

ConclusionUsing 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.

AbbreviationsSAGESerial Analysis of Gene Expression

LCMLaser Capture Microdissection

OCTOptimal Cutting Temperature

CVCresyl violet

DEPCDiethyl Pyrocarbonate

ABAAllen Brain Atlas

BACBacterial Artificial Chromosome

GENSATGene Expression Nervous System Atlas

UPGMAUnweighted Pair Group Method with Arithmetic Mean

EDExpression Divergence

GOGene Ontology.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2202-9-66 contains supplementary material, which is available to authorized users.

Cletus A D-Souza, Vikramjit Chopra contributed equally to this work.

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Author: Cletus A D-Souza - Vikramjit Chopra - Richard Varhol - Yuan-Yun Xie - Slavita Bohacec - Yongjun Zhao - Lisa LC Lee - Mikh

Source: https://link.springer.com/



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