Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting

Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting Shunsuke Suzuki1, Ryuichi Ono1, Takanori Narita2, Andrew J. Pask3, Geoffrey Shaw3, Changshan Wang1, Takashi Kohda1, Amber E. Alsop4, Jennifer A. Marshall Graves4, Yuji Kohara2, Fumitoshi Ishino1*, Marilyn B. Renfree3*, Tomoko Kaneko-Ishino5* 1 Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan, 2 Genome Biology Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan, 3 Department of Zoology, University of Melbourne, Victoria, Australia, 4 Research School of Biological Sciences, the Australian National University, Canberra, Australia, 5 School of Health Sciences, Tokai University, Bohseidai, Isehara, Kanagawa, Japan Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of- origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10) is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii), but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus), suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR) associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 59 region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation. Citation: Suzuki S, Ono R, Narita T, Pask AJ, Shaw G, et al. (2007) Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet 3(4): e55. doi:10.1371/journal.pgen.0030055 Introduction spongiotrophoblast and labyrinth layers leading to early embryonic lethality [18]. The origin of PEG10 is therefore of Genomic imprinting, or parent-of-origin-specific gene interest in view of its possible contribution to the evolution silencing, has been observed in both eutherian and marsupial, of mammalian placentation. Sequence identified as PEG10 but not monotreme mammals. In eutherians, more than 80 has recently been reported in the South American marsupial imprinted genes have been found and differential DNA the grey short-tailed opossum (Monodelphis domestica) [16] but methylation plays a crucial role in regulating their imprinted its precise location, genetic structure, and imprint status expression patterns [1–5]. In marsupials, three genes—IGF2, remains unknown. Here, we examined the PEG10 locus in two IGF2R, and PEG1/MEST—are imprinted, as they are in Australian mammals by isolating bacterial artificial chromo- eutherians, but no differentially methylated regions (DMRs) some (BAC) clones from a marsupial, the tammar wallaby, have been found in marsupials [6–8]. Consequently, the and from a monotreme, the platypus. regulatory mechanisms of genomic imprinting were thought to have evolved differently between marsupials and eutherians [6,8,9]. Results/Discussion It has been hypothesized that genomic imprinting arose as We used the tammar wallaby and the platypus as the a by-product of a DNA methylation mechanism that silences representative species of marsupials and monotremes, re- foreign DNAs [10], such as retrotransposons [11,12]. Sim- spectively, to compare with representative eutherians, the ilarly, transgenes can also become methylated, depending on human and the mouse. Several BAC clones were isolated from parent of origin, further supporting a link between genomic imprinting and silencing of foreign DNAs [13–15]. PEG10 is an imprinted gene sharing homology with the sushi-ichi Editor: Anne C. Ferguson-Smith, University of Cambridge, United Kingdom retrotransposon, and in humans and mice it has a clear Received November 22, 2006; Accepted February 26, 2007; Published April 13, DMR in its promoter region. Interestingly, PEG10 is 2007 conserved in eutherian mammals but not in nonmammalian Copyright: Ó 2007 Suzuki et al. This is an open-access article distributed under the vertebrates, such as birds and fish [11,16–18]. Therefore, terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author investigating the origin of the retrotransposon-derived and source are credited. PEG10 locus would clarify the relationship between retro- Abbreviations: BAC, bacterial artificial chromosome; DMR, differentially methy- transposon (or exogenous DNA sequence) insertion and lated region; LINES, long interspersed nuclear elements; LTR, long terminal repeat; genomic imprinting. SINES, short interspersed nuclear elements PEG10 is an essential placental gene in eutherians, since * To whom correspondence should be addressed. E-mail: [email protected]. knock-out mice have severe placental defects with loss of jp (FI); [email protected] (MBR); [email protected] (TKI) PLoS Genetics | www.plosgenetics.org0531 April 2007 | Volume 3 | Issue 4 | e55 Origin and Evolution of the PEG10 Imprinted Domain Author Summary 1A). The genetic structure of tammar PEG10 was also the same as that of eutherians, with two open reading frames Genomic imprinting is a gene regulatory mechanism controlling (ORFs) related to the sushi-ichi retrotransposon GAG and parent-of-origin-dependent expression of genes. In eutherians, POL proteins, respectively [11]. The CX2CX4HX4C RNA- imprinting is essential for fetal and placental development and binding motif of GAG and the DSG sequences of the defects in this mechanism are the cause of several genetic disorders. proteinase activation site of POL were also conserved (Figure In eutherian mammals, genomic imprinting is controlled by differ- S1). Tammar PEG10 was localised close to the telomere of ential methylation of the DNA. However, no such methylation- dependent mechanism had been previously identified in association Chromosome 3q, consistent with its autosomal location on with marsupial imprinting. By comparing the genome of all three proximal mouse Chromosome 6 (Figure 1B). However, in the extant classes of mammals (eutherians, marsupials, and monot- platypus, there were no PEG10 homologous sequences remes), we have investigated the evolution of PEG10 (paternally between SGCE and PPP1R9A (also called NEURABIN1) that expressed 10), a retrotransposon-derived imprinted gene that is flank PEG10 in other mammals (Figure 1A). essential for the formation of the placenta in the mouse. PEG10 was Using our tammar sequence and the published opossum present in a marsupial species, the tammar wallaby, but absent from genome sequence, we compared the entire region between an egg-laying monotreme species, the platypus. Therefore, PEG10 SGCE and PPP1R9A with the equivalent region in several was inserted into the genome at the time when the placenta and viviparity were evolving in therian mammals. This study has shown vertebrates from fish (fugu) to mammals. The size of this that PEG10 is not only imprinted in a marsupial, but that its imprint region in the platypus was similar to that of the chicken and is regulated by differential methylation, suggesting a common was smaller than in other mammals. There were numerous origin for methylation in the therian ancestor. These results provide long interspersed nuclear elements (LINEs) and short direct evidence that retrotransposon insertion can drive the interspersed nuclear elements (SINEs) (grey bars in Figure evolution of genomic imprinting in mammals. 1A) in all mammalian groups. A previous report suggests that there are less long terminal repeat (LTR)-type retrotransposon-derived sequences in the opossum and wallaby genomes tammar and platypus containing SGCE (sarcoglycan epsilon), [19], but a large number of these sequences were found in the neighboring gene of PEG10 in eutherians. DNA sequenc- this region as well as in mouse and human (blue bars in ing of one tammar BAC clone demonstrated the existence of Figure 1A). Consistent with the previous report, these were PEG10 and its conserved location adjacent to SGCE with absent in the platypus [19], as was PEG10. Most of the LTR- transcription occurring in a head-to-head manner (Figure type retrotransposon-derived sequences observed in these Figure 1. Comparison of the Genomic sStructures between SGCE and PPP1R9A, and Chromosomal Location for Tammar PEG10 (A) The green bars on the horizontal lines indicate the exons of each gene. Orthologous exons are connected between species by the broken lines. The grey bars on the upper side of the horizontal lines represent LINEs and SINEs, and the blue bars on the underside represent LTR elements. The arrowheads indicate the direction of transcription. The published opossum genome sequence used was PEG10 downstream, and was combined with our tammar genome sequence at the homologous

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