Divergent and nonuniform gene expression patterns in mouse brain

John A. Morris, Joshua J. Royall, Darren Bertagnolli, Andrew F. Boe, Josh J. Burnell, Emi J. Byrnes, Cathy Copeland, Tsega Desta, Shanna R. Fischer, Jeff Goldy, Katie J. Glattfelder, Jolene M. Kidney, Tracy Lemon, Geralyn J. Orta, Sheana E. Parry, Sayan D. Pathak, Owen C. Pearson, Melissa Reding, Sheila Shapouri, Kimberly A. SmithChad Soden, Beth M. Solan, John Weller, Joseph S. Takahashi, Caroline C. Overly, Ed S. Lein, Michael J. Hawrylycz, John G. Hohmann, Allan R. Jones

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs.

Original languageEnglish (US)
Pages (from-to)19049-19054
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number44
StatePublished - Nov 2 2010


  • Brain evolution;Gene regulation;Genetic background;Neuroanatomy;Species difference

ASJC Scopus subject areas

  • General


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