Abstract
BackgroundThere 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).ResultsUnexpected 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.ConclusionRadiation 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.
Highlights
There is only a limited understanding of the relation between copy number and expression for mammalian genes
Gene expression RNA was extracted from each of the 79 available radiation hybrid clones and technical replicates hybridized to Illumina HumanRef-8 v1.0 BeadChips
Assessing copy number and retention frequency in the G3 radiation hybrid (RH) panel To measure DNA copy number in the RH cell lines, we used array comparative genomic hybridization of each clone compared to the reference hamster A23 recipient line
Summary
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). Studies that map quantitative trait loci (QTLs) regulating gene expression (expression QTLs or eQTLs) usually rely on naturally occurring polymorphisms as a source of genetic variation and meiotic recombination to narrow down the regulatory loci. Since the variation in RH cells is due to CNVs, we refer to loci affecting expression in the RH panels copy number eQTLs or ceQTLs. unlike naturally occurring CNVs, variation in the RH panels is uniform and genome-wide
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