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MBE Advance Access published online on May 19, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn116
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Published by Oxford University Press 2008.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

Widespread ultraconservation divergence in primates

Ivan Ovcharenko

Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894

Email: ovcharei{at}ncbi.nlm.nih.gov

Received for publication March 14, 2008. Revision received April 25, 2008. Accepted for publication May 10, 2008.

The distribution and evolution of ultraconserved elements (UCEs, DNA stretches that are perfectly identical in primates and rodents) were examined in genomes of three primate species (human, chimpanzee, and rhesus macaque). It was found that the number of UCEs has decreased throughout primate evolution. At least 26% of ancestral UCEs have diverged in hominoids, while an additional 17% have accumulated one or more single nucleotide polymorphisms (SNPs) in the human genome. Sequence polymorphism analyses indicate that mutation fixation within an UCE can trigger a relaxation in the selective constraint on that element. Homogeneous mutation accumulations in UCEs served as a template by which purifying selection acted more effectively on protein-coding UCEs. Gene ontology annotation suggests that UCE sequence variation, primarily occurring in noncoding regions, might be linked to the reprogramming of the expression pattern of transcription factors and developmentally important genes. Many of these genes are expressed in the central nervous system. Finally, UCE sequence variability within human populations has been identified, including population-specific non-synonymous changes in protein-coding regions.


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L. Taher and I. Ovcharenko
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
Bioinformatics, March 1, 2009; 25(5): 578 - 584.
[Abstract] [Full Text] [PDF]


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