Characterisation of marsupial PHLDA2 reveals eutherian specific acquisition of imprinting

<p>Abstract</p> <p>Background</p> <p>Genomic imprinting causes parent-of-origin specific gene expression by differential epigenetic modifications between two parental genomes. We previously reported that there is no evidence of genomic imprinting of <it>CDKN1C </it>in the <it>KCNQ1 </it>domain in the placenta of an Australian marsupial, the tammar wallaby (<it>Macropus eugenii</it>) whereas tammar <it>IGF2 </it>and <it>H19</it>, located adjacent to the <it>KCNQ1 </it>domain in eutherian mammals, are imprinted. We have now identified and characterised the marsupial orthologue of <it>PHLDA2</it>, another gene in the <it>KCNQ1 </it>domain (also known as <it>IPL </it>or <it>TSSC3</it>) that is imprinted in eutherians. In mice, <it>Phlda2 </it>is a dose-sensitive negative regulator of placental growth, as <it>Cdkn1c </it>is for embryonic growth.</p> <p>Results</p> <p>Tammar <it>PHLDA2 </it>is highly expressed in the yolk sac placenta compared to other fetal tissues, confirming a similar expression pattern to that of mouse <it>Phlda2</it>. However, tammar <it>PHLDA2 </it>is biallelically expressed in both the fetus and yolk sac placenta, so it is not imprinted. The lack of imprinting in tammar <it>PHLDA2 </it>suggests that the acquisition of genomic imprinting of the <it>KCNQ1 </it>domain in eutherian mammals, accompanied with gene dosage reduction, occurred after the split of the therian mammals into the marsupials and eutherians.</p> <p>Conclusions</p> <p>Our results confirm the idea that acquisition of genomic imprinting in the <it>KCNQ1 </it>domain occurred specifically in the eutherian lineage after the divergence of marsupials, even though imprinting of the adjacent <it>IGF2-H19 </it>domain arose before the marsupial-eutherian split. These data are consistent with the hypothesis that genomic imprinting of the <it>KCNQ1 </it>domain may have contributed to the evolution of more complex placentation in the eutherian lineage by reduction of the gene dosage of negative regulators for both embryonic and placental growth.</p

Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting

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 5′ 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

Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes

Ono, R., Ishii, M., Fujihara, Y. et al. Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes. Sci Rep 5, 12281 (2015). https://doi.org/10.1038/srep1228

A trans-homologue interaction between reciprocally imprinted miR-127 and Rtl1 regulates placenta development.

The paternally expressed imprinted retrotransposon-like 1 (Rtl1) is a retrotransposon-derived gene that has evolved a function in eutherian placentation. Seven miRNAs, including miR-127, are processed from a maternally expressed antisense Rtl1 transcript (Rtl1as) and regulate Rtl1 levels through RNAi-mediated post-transcriptional degradation. To determine the relative functional role of Rtl1as miRNAs in Rtl1 dosage, we generated a mouse specifically deleted for miR-127. The miR-127 knockout mice exhibit placentomegaly with specific defects within the labyrinthine zone involved in maternal-fetal nutrient transfer. Although fetal weight is unaltered, specific Rtl1 transcripts and protein levels are increased in both the fetus and placenta. Phenotypic analysis of single (ΔmiR-127/Rtl1 or miR-127/ΔRtl1) and double (ΔmiR-127/ΔRtl1) heterozygous miR-127- and Rtl1-deficient mice indicate that Rtl1 is the main target gene of miR-127 in placental development. Our results demonstrate that miR-127 is an essential regulator of Rtl1, mediated by a trans-homologue interaction between reciprocally imprinted genes on the maternally and paternally inherited chromosomes.This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC) and EU FP7 Marie Curie Action 290123 (INGENIUM). This work was partly funded by a National Health and Medical Research Council (NHMRC) CJ Martin Biomedical Fellowship to A.N.S.P.This is the accepted manuscript. The final version is available at http://dev.biologists.org/content/early/2015/07/01/dev.121996.abstract

Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting

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 5′ 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

The Evolution of Mammalian Genomic Imprinting Was Accompanied by the Acquisition of Novel CpG Islands

Parent-of-origin–dependent expression of imprinted genes is mostly associated with allele-specific DNA methylation of the CpG islands (CGIs) called germ line differentially methylated regions (gDMRs). Although the essential role of gDMRs for genomic imprinting has been well established, little is known about how they evolved. In several imprinted loci, the CGIs forming gDMRs may have emerged with the insertion of a retrotransposon or retrogene. To examine the generality of the hypothesis that the CGIs forming gDMRs were novel CGIs recently acquired during mammalian evolution, we reviewed the time of novel CGI emergence for all the maternal gDMR loci using the novel data analyzed in this study combined with the data from previous reports. The comparative sequence analyses using mouse, human, dog, cow, elephant, tammar, opossum, platypus, and chicken genomic sequences were carried out for Peg13, Meg1/Grb10, Plagl1/Zac1, Gnas, and Slc38a4 imprinted loci to obtain comprehensive results. The combined data showed that emergence of novel CGIs occurred universally in the maternal gDMR loci at various time points during mammalian evolution. Furthermore, the analysis of Meg1/Grb10 locus provided evidence that gradual base pair–wise sequence change was involved in the accumulation of CpG sequence, suggesting the mechanism of novel CGI emergence is more complex than the suggestion that CpG sequences originated solely by insertion of CpG-rich transposable elements. We propose that acquisition of novel CGIs was a key genomic change for the evolution of imprinting and that it usually occurred in the maternal gDMR loci

In Vivo Function and Evolution of the Eutherian-Specific Pluripotency Marker UTF1

Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. UTF1 is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the UTF1 gene during mouse development. We found that homozygous UTF1 mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of UTF1 expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of UTF1 expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the UTF1 gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the UTF1 genes.This study was supported in part by the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT), and mostly by the Support Program for the Strategic Research Foundation at Private Universities, 2008–2012. This study was performed as a part of the Core Research for Evolutional Science and Technology (CREST) Agency. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

マウスモデルを用いたDOHaD検証系の確立：仔の行動表現型、遺伝子発現、ゲノムメチル化に関する網羅的解析

第3回日本DOHaD研究会学術集会　抄録集　【ポスター発表