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Human Molecular Genetics Advance Access published online on January 12, 2007
Human Molecular Genetics, doi:10.1093/hmg/ddl488
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© The Author 2007. Published by Oxford University Press. All rights reserved

Extreme context-specificity in differential allelic expression

James M. Wilkins, Lorraine Southam, Andrew J. Price, Zehra Mustafa, Andrew Carr and John Loughlin

University of Oxford, Institute of Musculoskeletal Sciences, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, OX3 7LD, United Kingdom

Corresponding author: James M. Wilkins, Fax 44 (0) 1865 227966, Tel. 44 (0) 1865 227963, Email: james.wilkins{at}ndos.ox.ac.uk

Received December 1, 2006; Accepted January 3, 2007

Variability in cis-regulation of gene expression has been implicated in the phenotypic manifestation of complex traits including common, multifactorial diseases. The differential expression of alleles due to polymorphism in cis-regulatory elements is common in the human genome, but there is a paucity of information about the context-specificity of these control elements. In this study, we examined the differential allelic expression (DAE) of BMP5 in human mesenchymal tissues obtained from 16 donors undergoing joint replacement for treatment of osteoarthritis. We observed significant differences in BMP5 allelic output, with allelic ratios greater than 4:1 (P < 10–20) in the tissues of some donors. We also discovered significant variability in allelic expression within the different tissues of donors. For 12 of our donors we examined the allelic expression of BMP5 in two different regions of cartilage: cartilage adjacent to the site of the osteoarthritic lesion and cartilage distal from the lesion. Five of these 12 donors demonstrated highly significant differences (P = 10–8) in allelic expression between the different regions of their cartilage. Using DAE as a phenotype, we attempted to map tissue-specific cis-regulatory polymorphisms, and we identified a single nucleotide polymorphism located downstream of BMP5 that was significantly associated with DAE in some but not all of the examined tissues. These findings suggest that allelic expression can be highly context-specific and that when interrogating the cis-regulatory control of a particular gene, one cannot necessarily assume that allelic expression is conserved across different tissues or even across different regions of the same tissue.


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