[1] Department of Molecular Genetics [2] Department of Computer Science [3] Banting and Best Department of Medical Research [4] Department of Immunology [5] Terrence Donnelly Centre for Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada, M5S 3E1 [6] Present address: Department of Biological Sciences, University of Calgary, 2500 University Drive, N.W., Calgary, AB, Canada, T2N 1N4 [7] Present address: Rosetta Inpharmatics, LLC, 401 Terry Avenue North, Seattle, WA, USA, 98109 *To whom correspondance should be addressed:
Background: Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet display extensive diversity in morphology, habitat, and behaviour. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates.
Results: We measured expression of all known and predicted genes across twenty tissues in chicken, frog and pufferfish. By combining the results with human and mouse data and considering only ten common tissues, we have found evidence of conserved expression for more than a third of unique orthologous genes. We find that, on average, transcription factor expression is neither more nor less conserved than other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved non-exonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes display conserved human/fish expression despite having virtually no nonexonic conserved primary sequence.
Conclusions: There are clearly strong evolutionary constraints on tissue-specific gene expression. A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis-regulatory restructuring.