Article abstract
Nature Genetics 41, 430 - 437 (2009)
Published online: 8 March 2009 | doi:10.1038/ng.350
The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells
Patrick Cahan1, Yedda Li1, Masayo Izumi1 & Timothy A Graubert1
Abstract
The extent to which differences in germline DNA copy number contribute to natural phenotypic variation is unknown. We analyzed the copy number content of the mouse genome to sub–10-kb resolution. We identified over 1,300 copy number variant regions (CNVRs), most of which are <10 kb in length, are found in more than one strain, and, in total, span 3.2% (85 Mb) of the genome. To assess the potential functional impact of copy number variation, we mapped expression profiles of purified hematopoietic stem and progenitor cells, adipose tissue and hypothalamus to CNVRs in cis. Of the more than 600 significant associations between CNVRs and expression profiles, most map to CNVRs outside of the transcribed regions of genes. In hematopoietic stem and progenitor cells, up to 28% of strain-dependent expression variation is associated with copy number variation, supporting the role of germline CNVs as key contributors to natural phenotypic variation in the laboratory mouse.
- Department of Internal Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St. Louis, Missouri, USA.
Correspondence to: Timothy A Graubert1 e-mail: graubert@wustl.edu
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