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

被引:18
作者
D'Souza, Cletus A. [1 ]
Chopra, Vikramjit [1 ]
Varhol, Richard [1 ]
Xie, Yuan-Yun [2 ,3 ]
Bohacec, Slavita [2 ,3 ]
Zhao, Yongjun [1 ]
Lee, Lisa L. C. [2 ,3 ]
Bilenky, Mikhail [1 ]
Portales-Casamar, Elodie [2 ,3 ]
He, An [1 ]
Wasserman, Wyeth W. [2 ,3 ]
Goldowitz, Daniel [2 ,3 ]
Marra, Marco A. [1 ]
Holt, Robert A. [2 ,3 ]
Simpson, Elizabeth M. [2 ,3 ]
Jones, Steven J. M. [1 ]
机构
[1] British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
[2] Univ British Columbia, Ctr Mol Med & Therapeut, Vancouver, BC V5Z 4H4, Canada
[3] Univ British Columbia, Child & Family Res Inst, Dept Med Genet, Vancouver, BC V5Z 4H4, Canada
关键词
D O I
10.1186/1471-2202-9-66
中图分类号
Q189 [神经科学];
学科分类号
071006 ;
摘要
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.
引用
收藏
页数:13
相关论文
共 41 条
  • [1] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [2] The significance of digital gene expression profiles
    Audic, S
    Claverie, JM
    [J]. GENOME RESEARCH, 1997, 7 (10): : 986 - 995
  • [3] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING
    BENJAMINI, Y
    HOCHBERG, Y
    [J]. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) : 289 - 300
  • [4] Berman JJ, 2003, ARCH PATHOL LAB MED, V127, P680
  • [5] Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models
    Brochier, Camille
    Gaillard, Marie-Claude
    Diguet, Elsa
    Caudy, Nicolas
    Dossat, Carole
    Segurens, Beatrice
    Wincker, Patrick
    Roze, Emmanuel
    Caboche, Jocelyne
    Hantraye, Philippe
    Brouillet, Emmanuel
    Elalouf, Jean-Marc
    de Chaldee, Michel
    [J]. PHYSIOLOGICAL GENOMICS, 2008, 33 (02) : 170 - 179
  • [6] Getting to the (c)ore of knowledge: mining biomedical literature
    de Bruijn, B
    Martin, J
    [J]. INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS, 2002, 67 (1-3) : 7 - 18
  • [7] Base-calling of automated sequencer traces using phred.: II.: Error probabilities
    Ewing, B
    Green, P
    [J]. GENOME RESEARCH, 1998, 8 (03): : 186 - 194
  • [8] Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions
    Fang, H
    Tong, WD
    Shi, LM
    Jakab, RL
    Bowyer, JF
    [J]. DNA AND CELL BIOLOGY, 2004, 23 (10) : 661 - 674
  • [9] SOMATODENDRITIC LOCALIZATION AND HYPERPHOSPHORYLATION OF TAU-PROTEIN IN TRANSGENIC MICE EXPRESSING THE LONGEST HUMAN BRAIN TAU-ISOFORM
    GOTZ, J
    PROBST, A
    SPILLANTINI, MG
    SCHAFER, T
    JAKES, R
    BURKI, K
    GOEDERT, M
    [J]. EMBO JOURNAL, 1995, 14 (07) : 1304 - 1313
  • [10] Mouse brain organization revealed through direct genome-scale TF expression analysis
    Gray, PA
    Fu, H
    Luo, P
    Zhao, Q
    Yu, J
    Ferrari, A
    Tenzen, T
    Yuk, DI
    Tsung, EF
    Cai, ZH
    Alerta, JA
    Cheng, LP
    Liu, Y
    Stenman, JM
    Valerius, MT
    Billings, N
    Kim, HA
    Greenberg, ME
    McMahon, AP
    Rowitch, DH
    Stiles, CD
    Ma, QF
    [J]. SCIENCE, 2004, 306 (5705) : 2255 - 2257