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This article is part of the supplement: ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011

Open Access Proceedings

Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution

Adriana Muñoz12* and David Sankoff2

Author affiliations

1 School of Information Technology & Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada

2 Department of Mathematics & Statistics, University of Ottawa, Ottawa, K1N 6N5, Canada

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Citation and License

BMC Bioinformatics 2012, 13(Suppl 3):S6  doi:10.1186/1471-2105-13-S3-S6

Published: 21 March 2012



We study the relation between genome rearrangements, breakpoints and gene expression. Genome rearrangement research has been concerned with the creation of breakpoints and their position in the chromosome, but the functional consequences of individual breakpoints remain virtually unknown, and there are no direct genome-wide studies of breakpoints from this point of view. A question arises of what the biological consequences of breakpoint creation are, rather than just their structural aspects. The question is whether proximity to the site of a breakpoint event changes the activity of a gene.


We investigate this by comparing the distribution of distances to the nearest breakpoint of genes that are differentially expressed with the distribution of the same distances for the entire gene complement. We study this in data on whole blood tissue in human versus macaque, and in cerebral cortex tissue in human versus chimpanzee. We find in both data sets that the distribution of distances to the nearest breakpoint of "changed expression genes" differs little from this distance calculated for the rest of the gene complement. In focusing on the changed expression genes closest to the breakpoints, however, we discover that several of these have previously been implicated in the literature as being connected to the evolutionary divergence of humans from other primates.


We conjecture that chromosomal rearrangements occasionally interrupt the regulatory configurations of genes close to the breakpoint, leading to changes in expression.