Regulatory element copy number differences shape primate expression profiles

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...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2012-07, Vol.109 (31), p.12656-12661
Main Authors: Iskow, Rebecca C, Gokcumen, Omer, Abyzov, Alexej, Malukiewicz, Joanna, Zhu, Qihui, Sukumar, Ann T, Pai, Athma A, Mills, Ryan E, Habegger, Lukas, Cusanovich, Darren A, Rubel, Meagan A, Perry, George H, Gerstein, Mark, Stone, Anne C, Gilad, Yoav, Lee, Charles
Format: Article
Language:English
Subjects:
Animals
Biological Sciences
Cell Line
Chimpanzees
conserved sequences
DNA, Intergenic - physiology
Evolution
Gene Dosage - physiology
Gene expression
Gene Expression Regulation - physiology
Genes
Genetic variation
Genomes
Genotype & phenotype
Humans
Macaca mulatta
Molecules
non-coding RNA
Pan troglodytes
Primates
Pseudogenes
Pseudogenes - physiology
Regulatory Elements, Transcriptional - physiology
Ribonucleic acid
RNA
RNA, Untranslated - physiology
Species Specificity
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1205199109