Regulatory element copy number differences shape primate expression profiles

Rebecca C. Iskow, Omer Gokcumen, Alexej Abyzov, Joanna Malukiewicz, Qihui Zhu, Ann T. Sukumar, Athma A. Pai, Ryan E. Mills, Lukas Habegger, Darren A. Cusanovich, Meagan A. Rubel, George H. Perry, Mark Gerstein, Anne C. Stone, Yoav Gilad, Charles Lee

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)12656-12661
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number31
DOIs
StatePublished - Jul 31 2012
Externally publishedYes

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Conserved Sequence
Primates
Long Noncoding RNA
Pseudogenes
Gene Dosage
Nucleic Acid Regulatory Sequences
Regulator Genes
Transcriptome
RNA
Gene Expression

Keywords

  • Copy number variation
  • Evolution
  • Genomics

ASJC Scopus subject areas

  • General

Cite this

Regulatory element copy number differences shape primate expression profiles. / 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.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 31, 31.07.2012, p. 12656-12661.

Research output: Contribution to journalArticle

Iskow, RC, Gokcumen, O, Abyzov, A, Malukiewicz, J, Zhu, Q, Sukumar, AT, Pai, AA, Mills, RE, Habegger, L, Cusanovich, DA, Rubel, MA, Perry, GH, Gerstein, M, Stone, AC, Gilad, Y & Lee, C 2012, 'Regulatory element copy number differences shape primate expression profiles', Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 31, pp. 12656-12661. https://doi.org/10.1073/pnas.1205199109
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. / Regulatory element copy number differences shape primate expression profiles. In: Proceedings of the National Academy of Sciences of the United States of America. 2012 ; Vol. 109, No. 31. pp. 12656-12661.
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