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Open Access Highly Accessed Research article

Effects of genome-wide copy number variation on expression in mammalian cells

Richard T Wang1, Sangtae Ahn25, Christopher C Park1, Arshad H Khan1, Kenneth Lange34 and Desmond J Smith1*

Author affiliations

1 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA

2 Department of Electrical Engineering, Signal and Image Processing Institute, School of Engineering, University of Southern California, Los Angeles, CA 90089, USA

3 Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA

4 Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA

5 GE Global Research Center, One Research Circle KW-C1308, Niskayuna, NY 12309, USA

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Citation and License

BMC Genomics 2011, 12:562  doi:10.1186/1471-2164-12-562

Published: 16 November 2011

Abstract

Background

There is only a limited understanding of the relation between copy number and expression for mammalian genes. We fine mapped cis and trans regulatory loci due to copy number change for essentially all genes using a human-hamster radiation hybrid (RH) panel. These loci are called copy number expression quantitative trait loci (ceQTLs).

Results

Unexpected findings from a previous study of a mouse-hamster RH panel were replicated. These findings included decreased expression as a result of increased copy number for 30% of genes and an attenuated relationship between expression and copy number on the X chromosome suggesting an Xist independent form of dosage compensation. In a separate glioblastoma dataset, we found conservation of genes in which dosage was negatively correlated with gene expression. These genes were enriched in signaling and receptor activities. The observation of attenuated X-linked gene expression in response to increased gene number was also replicated in the glioblastoma dataset. Of 523 gene deserts of size > 600 kb in the human RH panel, 325 contained trans ceQTLs with -log10 P > 4.1. Recently discovered genes, ultra conserved regions, noncoding RNAs and microRNAs explained only a small fraction of the results, suggesting a substantial portion of gene deserts harbor as yet unidentified functional elements.

Conclusion

Radiation hybrids are a useful tool for high resolution mapping of cis and trans loci capable of affecting gene expression due to copy number change. Analysis of two independent radiation hybrid panels show agreement in their findings and may serve as a discovery source for novel regulatory loci in noncoding regions of the genome.