A Regulatory Toolbox of MiniPromoters to Drive Selective Expression in the Brain

The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination "knockins" in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5' of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or in mouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type-specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies.

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References

Sandelin A, Alkema W, Engstrom P, Wasserman W, Lenhard B . JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2003; 32(Database issue):D91-4. PMC: 308747. DOI: 10.1093/nar/gkh012. View

Chatelin S, Wehrle R, Mercier P, Morello D, Sotelo C, Weber M . Neuronal promoter of human aromatic L-amino acid decarboxylase gene directs transgene expression to the adult floor plate and aminergic nuclei induced by the isthmus. Brain Res Mol Brain Res. 2001; 97(2):149-60. DOI: 10.1016/s0169-328x(01)00318-7. View

Lein E, Hawrylycz M, Ao N, Ayres M, Bensinger A, Bernard A . Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2006; 445(7124):168-76. DOI: 10.1038/nature05453. View

DSouza C, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y . Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008; 9:66. PMC: 2483290. DOI: 10.1186/1471-2202-9-66. View

Schoenherr C, Anderson D . Silencing is golden: negative regulation in the control of neuronal gene transcription. Curr Opin Neurobiol. 1995; 5(5):566-71. DOI: 10.1016/0959-4388(95)80060-3. View

Soriano P . Generalized lacZ expression with the ROSA26 Cre reporter strain. Nat Genet. 1999; 21(1):70-1. DOI: 10.1038/5007. View

Gong S, Zheng C, Doughty M, Losos K, Didkovsky N, Schambra U . A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature. 2003; 425(6961):917-25. DOI: 10.1038/nature02033. View

Yang G, Banks K, Bonaguro R, Wilson G, Dreolini L, de Leeuw C . Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus. Genomics. 2008; 93(3):196-204. DOI: 10.1016/j.ygeno.2008.09.014. View

Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson M, Ticoll A . PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol. 2007; 8(10):R207. PMC: 2246282. DOI: 10.1186/gb-2007-8-10-r207. View

10.

Carroll S . Evolution at two levels: on genes and form. PLoS Biol. 2005; 3(7):e245. PMC: 1174822. DOI: 10.1371/journal.pbio.0030245. View

11.

Mima K, Deguchi S, Yamauchi T . Characterization of 5' flanking region of alpha isoform of rat Ca2+/calmodulin-dependent protein kinase II gene and neuronal cell type specific promoter activity. Neurosci Lett. 2001; 307(2):117-21. DOI: 10.1016/s0304-3940(01)01941-3. View

12.

Strand A, Aragaki A, Baquet Z, Hodges A, Cunningham P, Holmans P . Conservation of regional gene expression in mouse and human brain. PLoS Genet. 2007; 3(4):e59. PMC: 1853119. DOI: 10.1371/journal.pgen.0030059. View

13.

Anderson G, Hagen S, Larson R, Strait K, Schwartz H, Mariash C . Purkinje cell protein-2 cis-elements mediate repression of T3-dependent transcriptional activation. Mol Cell Endocrinol. 1997; 131(1):79-87. DOI: 10.1016/s0303-7207(97)00095-6. View

14.

Visel A, Thaller C, Eichele G . GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2003; 32(Database issue):D552-6. PMC: 308763. DOI: 10.1093/nar/gkh029. View

15.

Coulon V, Lhonore A, Ouimette J, Dumontier E, van den Munckhof P, Drouin J . A muscle-specific promoter directs Pitx3 gene expression in skeletal muscle cells. J Biol Chem. 2007; 282(45):33192-200. DOI: 10.1074/jbc.M706119200. View

16.

Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K . Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005; 15(8):1034-50. PMC: 1182216. DOI: 10.1101/gr.3715005. View

17.

Wasserman W, Sandelin A . Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004; 5(4):276-87. DOI: 10.1038/nrg1315. View

18.

Farhadi H, Lepage P, Forghani R, Friedman H, Orfali W, Jasmin L . A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. J Neurosci. 2003; 23(32):10214-23. PMC: 6741010. View

19.

Kuduvalli P, Mitra R, Craig N . Site-specific Tn7 transposition into the human genome. Nucleic Acids Res. 2005; 33(3):857-63. PMC: 549396. DOI: 10.1093/nar/gki227. View

20.

Barnett S, Rosario M, Doyle A, Kilbey A, Lovatt A, Gillespie D . Differential regulation of AP-1 and novel TRE-specific DNA-binding complexes during differentiation of oligodendrocyte-type-2-astrocyte (O-2A) progenitor cells. Development. 1995; 121(12):3969-77. DOI: 10.1242/dev.121.12.3969. View