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Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

Andrew J Pask12*, Anthony T Papenfuss3, Eleanor I Ager1, Kaighin A McColl3, Terence P Speed3 and Marilyn B Renfree1

Author affiliations

1 Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia

2 Department of Molecular and Cellular Biology, The University of Connecticut, Storrs, CT 06269, USA

3 Bioinformatics Division, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3050, Australia

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Citation and License

Genome Biology 2009, 10:R1  doi:10.1186/gb-2009-10-1-r1

Published: 2 January 2009

Abstract

Background

Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals.

Results

We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus.

Conclusions

Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis.