Conservation of core gene expression in vertebrate tissues.
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.
Chan
Esther T
ET
Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada. esther.t.chan@gmail.com
Quon
Gerald T
GT
Chua
Gordon
G
Babak
Tomas
T
Trochesset
Miles
M
Zirngibl
Ralph A
RA
Aubin
Jane
J
Ratcliffe
Michael J H
MJ
Wilde
Andrew
A
Brudno
Michael
M
Morris
Quaid D
QD
Hughes
Timothy R
TR
D000818:Animals; D001001:Anura; D001483:Base Sequence; D002645:Chickens; D017124:Conserved Sequence / Q000235:genetics; D004247:DNA / Q000032:analysis / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D023721:Tetraodontiformes; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics; D014714:Vertebrates / Q000235:genetics / Q000378:metabolism
D014157:Transcription Factors; D004247:DNA