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Edited* by Rafael Palacios, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico, and approved June 15, 2012 (received for review April 2, 2012)
Abstract
Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
Footnotes
↵1R.C.I. and O.G. contributed equally to this work.
↵2Present address: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.
↵3Present address: Department of Computational Medicine and Bioinformatics and Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109.
↵4A.C.S., Y.G., and C.L. contributed equally to this work.
- ↵5To whom correspondence should be addressed. E-mail: clee{at}rics.bwh.harvard.edu.
Author contributions: R.C.I., O.G., R.E.M., G.H.P., M.G., A.C.S., Y.G., and C.L. designed research; R.C.I., O.G., J.M., A.T.S., and M.A.R. performed research; R.C.I., O.G., A.A., and Q.Z. contributed new reagents/analytic tools; R.C.I., O.G., A.A., Q.Z., A.A.P., L.H., and D.A.C. analyzed data; and R.C.I., O.G., and C.L. wrote the paper.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo [accession nos. GSE33960 (array comparative genomic hybridization) and GSE38572 (RNA sequencing data)].
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1205199109/-/DCSupplemental.
Copy number differences shape gene expression
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