- Open Access
Postnatal epigenetic reprogramming in the germline of a marsupial, the tammar wallaby
© Suzuki et al.; licensee BioMed Central Ltd. 2013
- Received: 11 January 2013
- Accepted: 8 May 2013
- Published: 3 June 2013
Epigenetic reprogramming is essential to restore totipotency and to reset genomic imprints during mammalian germ cell development and gamete formation. The dynamic DNA methylation change at DMRs (differentially methylated regions) within imprinted domains and of retrotransposons is characteristic of this process. Both marsupials and eutherian mammals have genomic imprinting but these two subgroups have been evolving separately for up to 160 million years. Marsupials have a unique reproductive strategy and deliver tiny, altricial young that complete their development within their mother's pouch. Germ cell proliferation in the genital ridge continues after birth in the tammar wallaby (Macropus eugenii), and it is only after 25 days postpartum that female germ cells begin to enter meiosis and male germ cells begin to enter mitotic arrest. At least two marsupial imprinted loci (PEG10 and H19) also have DMRs. To investigate the evolution of epigenetic reprogramming in the marsupial germline, here we collected germ cells from male pouch young of the tammar wallaby and analysed the methylation status of PEG10 and H19 DMR, an LTR (long terminal repeat) and a non-LTR retrotransposons.
Demethylation of the H19 DMR was almost completed by 14 days postpartum and de-novo methylation started from 34 days postpartum. These stages correspond to 14 days after the completion of primordial germ cell migration into genital ridge (demethylation) and 9 days after the first detection of mitotic arrest (re-methylation) in the male germ cells. Interestingly, the PEG10 DMR was already unmethylated at 7 days postpartum, suggesting that the timing of epigenetic reprogramming is not the same at all genomic loci. Retrotransposon methylation was not completely removed after the demethylation event in the germ cells, similar to the situation in the mouse.
Thus, despite the postnatal occurrence of epigenetic reprogramming and the persistence of genome-wide undermethylation for 20 days in the postnatal tammar, the relative timing and mechanism of germ cell reprogramming are conserved between marsupials and eutherians. We suggest that the basic mechanism of epigenetic reprogramming had already been established before the marsupial-eutherian split and has been faithfully maintained for at least 160 million years and may reflect the timing of the onset of mitotic arrest in the male germline.
- Epigenetic reprogramming
- Genomic imprinting
- Marsupial germ cells
- Germ cell methylation
Genome-wide dynamic changes of epigenetic states during mammalian germ cell development, called epigenetic reprogramming, are essential to restore totipotency and to renew parental imprinting in the male and female germ cells [1–4]. In mice, loss of DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) followed by the gain of H3K27me3 are the first gross epigenetic changes observed in migrating primordial germ cells (PGCs) between E7.5 and E9.5 [5, 6]. Then, the second wave of DNA demethylation which is associated with the erasure of parental imprinting, promoter methylation of germline genes and with the reduction of retrotransposon methylation takes place around E11.5, just after PGCs have entered into the genital ridges [7–10]. From E14.5, de-novo DNA methylation dependent on the actions of the DNMT3 family re-establishes paternal imprints and methylation of retrotransposons in G1-arrested male germ cells, known as prospermatogonia or male gonocytes [11–18].
In higher vertebrates, genomic imprinting has been identified in eutherian and marsupial mammals [19–24]. However, of the 16 or so eutherian imprinted genes examined so far in marsupials, only six are imprinted [23–35]. Furthermore, there are only two DMRs, associated with PEG10 and H19, that have been discovered so far, in marsupials, both in the tammar wallaby [24, 30]. The tammar H19 DMR was identified as a germline DMR because it was fully methylated in adult testes . However, the precise timing of epigenetic reprogramming in the developing germ cells of marsupials has never been established. Eutherians and marsupials have been evolving separately for up to 160 million years . Marsupials have a unique reproductive strategy and deliver tiny, altricial young that complete their development within their mother’s pouch . In the tammar, most PGCs complete their migration to the genital ridges just before birth . Post-migratory PGCs continue to proliferate after birth, and it is only after 25 days postpartum that female germ cells begin to enter meiosis while male germ cells enter into G1-phase mitotic arrest [39, 40]. To compare the evolution of epigenetic reprogramming between this distantly related mammal and the mouse, we analysed the methylation dynamics of the H19 DMR, which is the only paternal DMR discovered in marsupials so far, an LTR and a non-LTR retrotransposons in the male germline of the tammar wallaby during the postnatal proliferation and early mitotic arrest stages.
Isolation of germ cells from the tammar pouch young testes
DNA demethylation in the germline of tammar male pouch young
De-novo DNA methylation in the germline of tammar male pouch young
We next determined when de-novo methylation took place at the H19 DMR and the retrotransposons. At 20, 28, 32 and 33 days postpartum, the H19 DMR was still nearly fully unmethylated, suggesting that the undermethylated states observed at 14 days postpartum had persisted at least until these stages (Figure 3A). At the same time, these data demonstrate that the effect of somatic cell contamination during germ cell separation to the results of methylation analyses was negligible, so we assume the faint cut bands in the PEG10 DMR COBRA in Figures 1 and 4 may not be a simple reflection of somatic cell contamination. Also the methylation level of both LTR and non-LTR retrotransposons at 20 and 28 days postpartum was similar to that at 14 days postpartum (Figures 2B and C and 3A and B). On the other hand, we detected de-novo DNA methylation of the H19 DMR in three different animals at 34 days postpartum, indicating that 34 days postpartum is the critical stage for the acquisition of de-novo methylation and that it occurs rapidly. The increase of methylation in the retrotransposons was detected at 32 days postpartum, two days earlier than de-novo methylation of the H19 DMR (Figure 3A, B). It is possible that the methylation machinery responds more quickly to the retrotransposons retaining some degree of methylation than the fully unmethylated H19 DMR. Alternatively, the methylation machinery might be slightly differently recruited to the H19 DMR and to the retrotransposons. The G1-phase entry into mitotic arrest begins only after 25 days postpartum in the tammar male germline and is not complete until after day 50. Considering that germ cell development in the tammar wallaby takes much longer than in mouse and occurs postpartum, the relative timing and pattern of de-novo DNA methylation in the male germ cell development as well as the timing of demethylation is remarkably similar in both species. In mouse male germ cells undergoing mitotic arrest, NANOS2 maintains their arrested state and induces male-type germ cell differentiation including the expression of DNMT3L, an essential factor for the establishment of paternal imprinting and retrotransposon methylation . The orthologue of NANOS2 is found in the tammar genome (Hickford and Renfree, unpublished). Although the precise molecular pathway between NANOS2 and DNMT3L expression is still largely unknown, the similar relative timing of de-novo DNA methylation in the male germline of tammar and mouse, which starts shortly after the entry into mitotic arrest in both species, suggests that the molecular basis connecting these events has been conserved between marsupials and eutherians. The orthologues of the factors essential for paternal imprinting establishment in the mouse germline, such as DNMT3A, DNMT3L and BORIS/CTCFL, are also present in marsupials [48, 49]. These orthologues most likely play the same critical role to establish the methylation imprint in the marsupial H19 DMR, which occurs at a similar relative time in the male germ cell development as in that of the mouse.
Demethylation and de-novo methylation in the male germline of a marsupial occurs over a prolonged period postpartum. Despite the occurrence of epigenetic reprogramming postnatally and the persistence of genome-wide undermethylation for 20 days in the postnatal tammar, the relative timing and mechanism of germ cell reprogramming was conserved between marsupials and eutherians. We suggest that the basic mechanism of epigenetic reprogramming had already been established before the marsupial-eutherian split and has been faithfully maintained for at least 160 million years and that it is tightly correlated with the onset of mitotic arrest in the male tammar wallaby.
Animals and tissue collection
Tammar wallabies (Macropus eugenii) of Kangaroo Island origin were maintained in our breeding colony in grassy, outdoor enclosures. Lucerne cubes, grass and water were provided ad libitum and supplemented with fresh vegetables. Gonads or testes were collected from pouch young aged between 1 and 34 days postpartum. The pouch young age was determined by plotting head length against growth curves for the tammar . Experimental procedures conformed to Australian National Health and Medical Research Council (2004) guidelines and were approved by the Animal Experimentation Ethics Committees of the University of Melbourne.
Preparation of single cell suspension
Gonads or testes were torn using a needle in 0.25% Trypsin/EDTA (Invitrogen) and were incubated for 10 min at 37°C. The gonadal/testicular cells were dissociated by 30 pipetting strokes with 1 mL plastic tips followed by 10 strokes with 200 μL plastic tips. The cell samples were passed through 40 μm cell strainer (BD Biosciences).
Germ cell labeling
The cells were fixed in 4% PFA/PBS for 20 min at room temperature and then permeabilised in 0.1% Triton X-100/PBS for 15 min at room temperature. The primary antibody reactions were performed in 0.1% BSA and 0.05% Tween 20/PBS containing the SSEA1 antibody (1/30 of total reaction volume, MC-480; Developmental Studies Hybridoma Bank at the University of Iowa) or the DDX4/VASA antibody (1/300 of total reaction volume, ab13840; Abcam) for 30 min at room temperature. The cells were washed in 0.1% Tween 20/PBS and were labeled by the secondary antibodies (Invitrogen) in the same solution as the primary antibody reaction. The labeled single cell suspension samples were passed through 40 μm cell strainer (BD Biosciences) before fluorescence activated cell sorting, FACS (MoFlo Cell Sorter, Beckman Coulter and FACS Aria III, BD Biosciences).
DNA methylation analyses
Genomic DNA was extracted from the germ cells collected by FACS using a Wizard Genomic DNA Purification Kit (Promega). Purified genomic DNA was treated with a sodium bisulphite solution as described previously [60, 61]. After the bisulphite treatment for the genomic DNA, 30 to 38 cycles of PCR with the genomic DNA templates corresponding to 100 to 5,000 cells were carried out using the following primer pairs.
PEG10 DMR Forward: 5′- CCTCCCATTAACTTTAAAATCACC -3′
PEG10 DMR Reverse: 5′- ATTGTAGTAATGGGGTAGGTTATG -3′
H19 DMR Forward: 5′- GAATGGGTTAGATGAGGGTAGTATAG -3′
H19 DMR Reverse: 5′- TATCAAACACCAAAACCACAAATAA -3′
H19 COBRA Forward: 5′- TTATTTTGGAGAAAATTTGAAGATAAGTAG -3′
H19 COBRA Reverse: 5′- TATCCTAAAACATCAAAACCTAAATTAAAC -3′
KERV-1 LTR Forward: 5′- TAAACTCAATTCCATATAAACAATCTC -3′
KERV-1 LTR Reverse: 5′- TTTTTGTTTTGTAAGGGTTTTTTAG -3′
LINE1 Forward: 5′- GGAGATTTTTGTTTTAGAGAGATTTGTAAA -3′
LINE1 Reverse: 5′- TATAAAAACACCCCACTCCCCTCTC -3′
The PCR products for COBRA (combined bisulphite and restriction analysis) were digested with 1 to 10 units of MluCI, AciI, TaqI (New England Biolabs) or HinfI (TaKaRa) restriction enzymes for 2-3 h at 37°C or 65°C for TaqI. The intensity of the cut and uncut bands was quantified by ATTO CS Analyzer 3 software (ATTO). The PCR products for H19 DMR and retrotransposons were cloned, and the clones were sequenced. The sequence data were analysed by QUMA (quantification tool for methylation analysis; http://quma.cdb.riken.jp) .
We thank Alison Bradfield and Scott Brownlees for assistance with the animals, Helen Clark and Bonnie Dopheide for technical assistance and Drs. Hongshi Yu and Danielle Hickford for help in collecting tissue. Fluorescence activated cell sorting was operated by Dr. Matt Burton at Murdoch Children’s Research Institute, Royal Children's Hospital and Susumu Ito at Research Center for Human and Environmental Sciences, Shinshu University.
- Hackett JA, Zylicz JJ, Surani MA: Parallel mechanisms of epigenetic reprogramming in the germline. Trends Genet. 2012, 28: 164-174. 10.1016/j.tig.2012.01.005.View ArticlePubMedGoogle Scholar
- Saitou M, Kagiwada S, Kurimoto K: Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development. 2012, 139: 15-31. 10.1242/dev.050849.View ArticlePubMedGoogle Scholar
- Sasaki H, Matsui Y: Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet. 2008, 9: 129-140. 10.1038/ni1560.View ArticlePubMedGoogle Scholar
- Reik W: Stability and flexibility of epigenetic gene regulation in mammalian development. Nature. 2007, 447: 425-432. 10.1038/nature05918.View ArticlePubMedGoogle Scholar
- Seki Y, Hayashi K, Itoh K, Mizugaki M, Saitou M, Matsui Y: Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol. 2005, 278: 440-458. 10.1016/j.ydbio.2004.11.025.View ArticlePubMedGoogle Scholar
- Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, Saga Y, Tachibana M, Shinkai Y, Saitou M: Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development. 2007, 134: 2627-2638. 10.1242/dev.005611.View ArticlePubMedGoogle Scholar
- Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA: Epigenetic reprogramming in mouse primordial germ cells. Mech Dev. 2002, 117: 15-23. 10.1016/S0925-4773(02)00181-8.View ArticlePubMedGoogle Scholar
- Lane N, Dean W, Erhardt S, Hajkova P, Surani A, Walter J, Reik W: Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis. 2003, 35: 88-93. 10.1002/gene.10168.View ArticlePubMedGoogle Scholar
- Lee J, Inoue K, Ono R, Ogonuki N, Kohda T, Kaneko-Ishino T, Ogura A, Ishino F: Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development. 2002, 129: 1807-1817.View ArticlePubMedGoogle Scholar
- Maatouk DM, Kellam LD, Mann MR, Lei H, Li E, Bartolomei MS, Resnick JL: DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. Development. 2006, 133: 3411-3418. 10.1242/dev.02500.View ArticlePubMedGoogle Scholar
- Bourc'his D, Bestor TH: Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature. 2004, 431: 96-99. 10.1038/nature02886.View ArticlePubMedGoogle Scholar
- Davis TL, Trasler JM, Moss SB, Yang GJ, Bartolomei MS: Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis. Genomics. 1999, 58: 18-28. 10.1006/geno.1999.5813.View ArticlePubMedGoogle Scholar
- Davis TL, Yang GJ, McCarrey JR, Bartolomei MS: The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet. 2000, 9: 2885-2894. 10.1093/hmg/9.19.2885.View ArticlePubMedGoogle Scholar
- Kaneda M, Okano M, Hata K, Sado T, Tsujimoto N, Li E, Sasaki H: Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature. 2004, 429: 900-903. 10.1038/nature02633.View ArticlePubMedGoogle Scholar
- Kato Y, Kaneda M, Hata K, Kumaki K, Hisano M, Kohara Y, Okano M, Li E, Nozaki M, Sasaki H: Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet. 2007, 16: 2272-2280. 10.1093/hmg/ddm179.View ArticlePubMedGoogle Scholar
- Li JY, Lees-Murdock DJ, Xu GL, Walsh CP: Timing of establishment of paternal methylation imprints in the mouse. Genomics. 2004, 84: 952-960. 10.1016/j.ygeno.2004.08.012.View ArticlePubMedGoogle Scholar
- Webster KE, O’Bryan MK, Fletcher S, Crewther PE, Aapola U, Craig J, Harrison DK, Aung H, Phutikanit N, Lyle R, Meachem SJ, Antonarakis SE, de Kretser DM, Hedger MP, Peterson P, Carroll BJ, Scott HS: Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci U S A. 2005, 102: 4068-4073. 10.1073/pnas.0500702102.PubMed CentralView ArticlePubMedGoogle Scholar
- Ueda T, Abe K, Miura A, Yuzuriha M, Zubair M, Noguchi M, Niwa K, Kawase Y, Kono T, Matsuda Y, Fujimoto H, Shibata H, Hayashizaki Y, Sasaki H: The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development. Genes Cells. 2000, 5: 649-659. 10.1046/j.1365-2443.2000.00351.x.View ArticlePubMedGoogle Scholar
- Hore TA, Rapkins RW, Graves JA: Construction and evolution of imprinted loci in mammals. Trends Genet. 2007, 23: 440-448. 10.1016/j.tig.2007.07.003.View ArticlePubMedGoogle Scholar
- Renfree MB, Ager EI, Shaw G, Pask AJ: Genomic imprinting in marsupial placentation. Reproduction. 2008, 136: 523-531. 10.1530/REP-08-0264.View ArticlePubMedGoogle Scholar
- Renfree MB, Hore TA, Shaw G, Graves JA, Pask AJ: Evolution of genomic imprinting: insights from marsupials and monotremes. Annu Rev Genomics Hum Genet. 2009, 10: 241-262. 10.1146/annurev-genom-082908-150026.View ArticlePubMedGoogle Scholar
- Reik W, Lewis A: Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet. 2005, 6: 403-410.View ArticlePubMedGoogle Scholar
- Suzuki S, Renfree MB, Pask AJ, Shaw G, Kobayashi S, Kohda T, Kaneko-Ishino T, Ishino F: Genomic imprinting of IGF2, p57(KIP2) and PEG1/MEST in a marsupial, the tammar wallaby. Mech Dev. 2005, 122: 213-222. 10.1016/j.mod.2004.10.003.View ArticlePubMedGoogle Scholar
- Suzuki S, Ono R, Narita T, Pask AJ, Shaw G, Wang C, Kohda T, Alsop AE, Marshall Graves JA, Kohara Y, Ishino F, Renfree MB, Kaneko-Ishino T: Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet. 2007, 3: e55-10.1371/journal.pgen.0030055.PubMed CentralView ArticlePubMedGoogle Scholar
- Killian JK, Byrd JC, Jirtle JV, Munday BL, Stoskopf MK, MacDonald RG, Jirtle RL: M6P/IGF2R imprinting evolution in mammals. Mol Cell. 2000, 5: 707-716. 10.1016/S1097-2765(00)80249-X.View ArticlePubMedGoogle Scholar
- O'Neill MJ, Ingram RS, Vrana PB, Tilghman SM: Allelic expression of IGF2 in marsupials and birds. Dev Genes Evol. 2000, 210: 18-20. 10.1007/PL00008182.View ArticlePubMedGoogle Scholar
- Rapkins RW, Hore T, Smithwick M, Ager E, Pask AJ, Renfree MB, Kohn M, Hameister H, Nicholls RD, Deakin JE, Graves JA: Recent assembly of an imprinted domain from non-imprinted components. PLoS Genet. 2006, 2: e182-10.1371/journal.pgen.0020182.PubMed CentralView ArticlePubMedGoogle Scholar
- Ager E, Suzuki S, Pask A, Shaw G, Ishino F, Renfree MB: Insulin is imprinted in the placenta of the marsupial. Macropus eugenii. Dev Biol. 2007, 309: 317-328. 10.1016/j.ydbio.2007.07.025.View ArticlePubMedGoogle Scholar
- Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, Dunham I, Renfree MB, Ferguson-Smith AC, SAVOIR consortium: The evolution of the DLK1-DIO3 imprinted domain in mammals. PLoS Biol. 2008, 6: e135-10.1371/journal.pbio.0060135.PubMed CentralView ArticlePubMedGoogle Scholar
- Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL, McCarrey JR, Renfree MB, Reik W, Dunham I, SAVOIR consortium: Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat Genet. 2008, 40: 971-976. 10.1038/ng.168.View ArticlePubMedGoogle Scholar
- Suzuki S, Shaw G, Kaneko-Ishino T, Ishino F, Renfree MB: Characterisation of marsupial PHLDA2 reveals eutherian specific acquisition of imprinting. BMC Evol Biol. 2011, 11: 244-10.1186/1471-2148-11-244.PubMed CentralView ArticlePubMedGoogle Scholar
- Suzuki S, Shaw G, Kaneko-Ishino T, Ishino F, Renfree MB: The evolution of mammalian genomic imprinting was accompanied by the acquisition of novel CpG islands. Genome Biol Evol. 2011, 3: 1276-1283. 10.1093/gbe/evr104.PubMed CentralView ArticlePubMedGoogle Scholar
- Stringer JM, Suzuki S, Pask AJ, Shaw G, Renfree MB: GRB10 imprinting is eutherian mammal specific. Mol Biol Evol. 2012, 29: 3711-3719. 10.1093/molbev/mss173.View ArticlePubMedGoogle Scholar
- Stringer JM, Suzuki S, Pask AJ, Shaw G, Renfree MB: Promoter-specific expression and imprint status of marsupial IGF2. PLoS One. 2012, 7: e41690-10.1371/journal.pone.0041690.PubMed CentralView ArticlePubMedGoogle Scholar
- Stringer JM, Suzuki S, Pask AJ, Shaw G, Renfree MB: Selected imprinting of INS in the marsupial. Epigenetics Chromatin. 2012, 5: 14-10.1186/1756-8935-5-14.PubMed CentralView ArticlePubMedGoogle Scholar
- Luo ZX, Yuan CX, Meng QJ, Ji Q: A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature. 2011, 476: 442-445. 10.1038/nature10291.View ArticlePubMedGoogle Scholar
- Tyndale-Biscoe CH, Renfree MB: Monographs on Marsupial Biology: Reproductive physiology of marsupials. 1987, Cambridge: Cambridge University PressView ArticleGoogle Scholar
- Ullmann SL, Shaw G, Alcorn GT, Renfree MB: Migration of primordial germ cells to the developing gonadal ridges in the tammar wallaby Macropus eugenii. J Reprod Fertil. 1997, 110: 135-143. 10.1530/jrf.0.1100135.View ArticlePubMedGoogle Scholar
- Alcorn GT, Robinson ES: Germ cell development in female pouch young of the tammar wallaby (Macropus eugenii). J Reprod Fertil. 1983, 67: 319-325. 10.1530/jrf.0.0670319.View ArticlePubMedGoogle Scholar
- Renfree MBOWS, Short RV, Shaw G: Sexual differentiation of the urogenital system of the fetal and neonatal tammar wallaby, Macropus eugenii. Anat Embryol (Berl). 1996, 194: 111-134.View ArticleGoogle Scholar
- Hickford DE, Frankenberg S, Pask AJ, Shaw G, Renfree MB: DDX4 (VASA) is conserved in germ cell development in marsupials and monotremes. Biol Reprod. 2011, 85: 733-743. 10.1095/biolreprod.111.091629.View ArticlePubMedGoogle Scholar
- Hickford D, Frankenberg S, Renfree MB: Immunohistochemical staining of sectioned tammar wallaby (Macropus eugenii) tissue. Cold Spring Harb Protoc. 2009, 2009: pdb.prot5338-10.1101/pdb.prot5338.PubMedGoogle Scholar
- Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A: The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One. 2010, 5: e8888-10.1371/journal.pone.0008888.PubMed CentralView ArticlePubMedGoogle Scholar
- Jin SG, Kadam S, Pfeifer GP: Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010, 38: e125-10.1093/nar/gkq223.PubMed CentralView ArticlePubMedGoogle Scholar
- Nestor C, Ruzov A, Meehan R, Dunican D: Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques. 2010, 48: 317-319. 10.2144/000113403.View ArticlePubMedGoogle Scholar
- Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, Surani MA: Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science. 2013, 339: 448-452. 10.1126/science.1229277.View ArticlePubMedGoogle Scholar
- Saga Y: Sexual development of mouse germ cells: Nanos2 promotes the male germ cell fate by suppressing the female pathway. Dev Growth Differ. 2008, Suppl 1: S141-S147.View ArticleGoogle Scholar
- Yokomine T, Hata K, Tsudzuki M, Sasaki H: Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet Genome Res. 2006, 113: 75-80. 10.1159/000090817.View ArticlePubMedGoogle Scholar
- Hore TA, Deakin JE, Marshall Graves JA: The evolution of epigenetic regulators CTCF and BORIS/CTCFL in amniotes. PLoS Genet. 2008, 4: e1000169-10.1371/journal.pgen.1000169.PubMed CentralView ArticlePubMedGoogle Scholar
- Pillai RS, Chuma S: piRNAs and their involvement in male germline development in mice. Dev Growth Differ. 2012, 54: 78-92. 10.1111/j.1440-169X.2011.01320.x.View ArticlePubMedGoogle Scholar
- Hackett JA, Reddington JP, Nestor CE, Dunican DS, Branco MR, Reichmann J, Reik W, Surani MA, Adams IR, Meehan RR: Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development. 2012, 139: 3623-3632. 10.1242/dev.081661.PubMed CentralView ArticlePubMedGoogle Scholar
- Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tushl T: A novel class of small RNAs bind to MILI protein in mouse testes. Nature. 2006, 442: 203-207.PubMedGoogle Scholar
- Girard A, Sachidanandam R, Hannon GJ, Carmell MA: A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature. 2006, 442: 199-202.PubMedGoogle Scholar
- Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ: Developmentally regulated piRNA clusters implicate MILI in transposon control. Science. 2007, 316: 744-747. 10.1126/science.1142612.View ArticlePubMedGoogle Scholar
- Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y, Ijiri TW, Hata K, Li E, Matsuda Y, Kimura T, Okabe M, Sakaki Y, Sasaki H, Nakano T: DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 2008, 22: 908-917. 10.1101/gad.1640708.PubMed CentralView ArticlePubMedGoogle Scholar
- Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, Shiromoto Y, Asada N, Toyoda A, Fujiyama A, Totoki Y, Shibata T, Kimura T, Nakatsuji N, Noce T, Sasaki H, Nakano T: MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 2010, 24: 887-892. 10.1101/gad.1902110.PubMed CentralView ArticlePubMedGoogle Scholar
- Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefevre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011, 12: R81-10.1186/gb-2011-12-8-r81.PubMed CentralView ArticlePubMedGoogle Scholar
- Ollinger R, Childs AJ, Burgess HM, Speed RM, Lundegaard PR, Reynolds N, Gray NK, Cooke HJ, Adams IR: Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice. PLoS Genet. 2008, 4: e1000199-10.1371/journal.pgen.1000199.PubMed CentralView ArticlePubMedGoogle Scholar
- Poole WE, Simms NG, Wood JT, Lubulwa M: Tables for age determination of the Kangaroo Island wallaby (Tammar), Macropus eugenii, from body measurements. 1991, Canberra: Australia Division of Wildlife and EcologyGoogle Scholar
- Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL: A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992, 89: 1827-1831. 10.1073/pnas.89.5.1827.PubMed CentralView ArticlePubMedGoogle Scholar
- Raizis AM, Schmitt F, Jost JP: A bisulfite method of 5-methylcytosine mapping that minimizes template degradation. Anal Biochem. 1995, 226: 161-166. 10.1006/abio.1995.1204.View ArticlePubMedGoogle Scholar
- Kumaki Y, Oda M, Okano M: QUMA: quantification tool for methylation analysis. Nucleic Acids Res. 2008, 36 (Web Server issue): 170-175.View ArticleGoogle Scholar
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