Research article

Conservation of core gene expression in vertebrate tissues

Esther T Chan^1,5 , Gerald T Quon^2,5 , Gordon Chua^3,5,6 , Tomas Babak^5,7 , Miles Trochesset^2,3 , Ralph A Zirngibl¹ , Jane Aubin¹ , Michael JH Ratcliffe⁴ , Andrew Wilde¹ , Michael Brudno^2,3,5 , Quaid D Morris^1,2,3,5 and Timothy R Hughes^1,3,5

¹  Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

²  Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

³  Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

⁴  Department of Immunology and Sunnybrook Research Institute, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

⁵  Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

⁶  Current address: Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4 Canada

⁷  Current address: Rosetta Inpharmatics, 401 Terry Avenue North, Seattle, WA 98109, USA

author email corresponding author email

Journal of Biology 2009, 8:33doi:10.1186/jbiol130

Published:	16 April 2009

Abstract

Background

Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. 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 gene expression is neither more nor less conserved than that of other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved nonexonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes show conserved human/fish expression despite having almost 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.