The Pleiades Promoter Project: Using bioinformatics to design human DNA MiniPromoters driving region-specific expression in the brain.
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1
The University of British Columbia, Canada
Alzheimer Disease, Parkinson Disease, and depression represent an enormous social and economic burden and a major unmet treatment need. However, gene therapy directly or via stem cells, holds great therapeutic promise. The Pleiades Promoter Project (www.pleiades.org) is generating a public resource of 160 fully characterized, human DNA MiniPromoters to drive gene expression in defined brain regions of therapeutic interest.
Our approach relies on the observation that tissue-specific expression is often mediated by regulatory regions, so called cis-regulatory modules or CRMs, acting in a modular fashion to control the activity of a promoter (Yuh et al., Development, 2001). For instance, a ~500 bp sequence ~9 kb upstream of the Myelin Basic Protein gene is sufficient to drive specific expression to Schwann cells when inserted adjacent to a heterologous promoter driving a lacZ reporter gene (Farhadi et al., JNeurosci, 2003).
In the Pleiades Promoter Project, we are taking a genome wide approach to identify candidate genes with region-specific expression patterns in the brain, using existing genomic expression database resources (e.g. Allen brain atlas, GENSAT). We then identify putative CRMs for those genes using a range of informatics tools: (i) detailed curation of the literature using the PAZAR database (www.pazar.info); (ii) phylogenetic footprinting under the assumption that functional regulatory regions are retained over evolutionary time; and (iii) transcription factor (TF) binding site predictions when relevant TFs are known. For each gene, four MiniPromoter constructs, shorter than 4 kb, are being generated, allowing for testing of different combinations of CRMs. Each promoter is cloned 5' of the EGFP reporter and introduced into the Hprt genomic locus by homologous recombination gene-targeting in mouse embryonic stem cells. A total of 205 new promoter-EGFP strains of knock-in mice are being generated. Detailed histological analyses of the brain are conducted to document the region and cell-type specificity of these MiniPromoters; results are provided through an online visualization system.
This integrative approach has the potential to produce valuable spatially-restricted expression tools for both gene therapy and applied research. Most significantly, this project will provide insights into the modular organization of regulatory regions and the complex gene regulatory programs of the brain. All data will be publicly available along with mice and intermediate resources to establish a ‘tool-kit’ for the scientific community.
Conference:
Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008.
Presentation Type:
Poster and Short Oral Presentation
Topic:
Genomics and Genetics
Citation:
Portales-Casamar
E,
Swanson
M,
Holt
R,
Goldowitz
D,
Jones
S,
Simpson
E and
Wasserman
W
(2008). The Pleiades Promoter Project: Using bioinformatics to design human DNA MiniPromoters driving region-specific expression in the brain..
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2008.
doi: 10.3389/conf.neuro.11.2008.01.078
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Received:
28 Jul 2008;
Published Online:
28 Jul 2008.
*
Correspondence:
Elodie Portales-Casamar, The University of British Columbia, Vancouver, Canada, elodie@cmmt.ubc.ca