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Open Access Highly Accessed Research article

Retrocopy contributions to the evolution of the human genome

Robert Baertsch1*, Mark Diekhans1, W James Kent1, David Haussler1 and Jürgen Brosius2

Author affiliations

1 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA

2 Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149, Münster, Germany

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Citation and License

BMC Genomics 2008, 9:466  doi:10.1186/1471-2164-9-466

Published: 8 October 2008

Abstract

Background

Evolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. By contrast, 45% of the human genome is composed of retroposed elements, many of which were inserted in the primate lineage. A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes.

Results

To identify and analyze the relatively recently evolved retrogenes, we carried out BLASTZ alignments of all human mRNAs against the human genome and scored a set of features indicative of retroposition. Of over 12,000 putative retrocopy-derived genes that arose mainly in the primate lineage, 726 with strong evidence of transcript expression were examined in detail. These mRNA retroposition events fall into three categories: I) 34 retrocopies and antisense retrocopies that added potential protein coding space and UTRs to existing genes; II) 682 complete retrocopy duplications inserted into new loci; and III) an unexpected set of 13 retrocopies that contributed out-of-frame, or antisense sequences in combination with other types of transposed elements (SINEs, LINEs, LTRs), even unannotated sequence to form potentially novel genes with no homologs outside primates. In addition to their presence in human, several of the gene candidates also had potentially viable ORFs in chimpanzee, orangutan, and rhesus macaque, underscoring their potential of function.

Conclusion

mRNA-derived retrocopies provide raw material for the evolution of genes in a wide variety of ways, duplicating and amending the protein coding region of existing genes as well as generating the potential for new protein coding space, or non-protein coding RNAs, by unexpected contributions out of frame, in reverse orientation, or from previously non-protein coding sequence.