Open Access Research article

Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background

Harry A Noyes1, Morris Agaba2, Susan Anderson4, Alan L Archibald4, Andy Brass5, John Gibson26, Laurence Hall4, Helen Hulme5, Sung Jong Oh3 and Stephen Kemp12*

Author Affiliations

1 School of Biological Sciences, University of Liverpool, Liverpool, UK

2 Biotechnology Theme, International Livestock Research Institute, Nairobi, Kenya

3 National Institute of Animal Science, Rural Development Administration, Suwon, Korea

4 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Scotland, UK

5 School of Computer Science/Faculty of Life Sciences, University of Manchester, Manchester, UK

6 School of Science and Technology, University of New England, Armidale, New South Wales, Australia

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BMC Genomics 2010, 11:361  doi:10.1186/1471-2164-11-361

Published: 7 June 2010



Differences in gene expression may be caused by nearby DNA polymorphisms (cis regulation) or by interactions of gene control regions with polymorphic transcription factors (trans regulation). Trans acting loci are much harder to detect than cis acting loci and their effects are much more sensitive to genetic background.


To quantify cis and trans regulation we correlated haplotype data with gene expression in two inbred mouse strains and two derived congenic lines. Upstream haplotype differences between the parental strains suggested that 30-43% of differentially expressed genes were differentially expressed because of cis haplotype differences. These cis regulated genes displayed consistent and relatively tissue-independent differential expression. We independently estimated from the congenic mice that 71-85% of genes were trans regulated. Cis regulated genes were associated with low p values (p < 0.005) for differential expression, whereas trans regulated genes were associated with values 0.005 < p < 0.05. The genes differentially expressed between congenics and controls were not a subset of those that were differentially expressed between the founder lines, showing that these were dependent on genetic background. For example, the cholesterol synthesis pathway was strongly differentially expressed in the congenic mice by indirect trans regulation but this was not observable in the parental mice.


The evidence that most gene regulation is trans and strongly influenced by genetic background, suggests that pathways that are modified by an allelic variant, may only exhibit differential expression in the specific genetic backgrounds in which they were identified. This has significant implications for the interpretation of any QTL mapping study.