Dimethylated histone H3 lysine 9 is dispensable for the interaction between developmental pluripotency-associated protein 3 (Dppa3) and ten-eleven translocation 3 (Tet3) in somatic cells
Qian-Qian Wang A , Yu-Mei Zhang A , Xia Zhong A , Jian-Wei Li A , Xiao-Rong An A and Jian Hou A BA State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China.
B Corresponding author. Email: houjian@cau.edu.cn
Reproduction, Fertility and Development 31(2) 347-356 https://doi.org/10.1071/RD18062
Submitted: 30 November 2017 Accepted: 11 July 2018 Published: 13 August 2018
Abstract
Both developmental pluripotency-associated protein 3 (Dppa3/Stella/PGC7) and dioxygenase ten-eleven translocation 3 (Tet3) are maternal factors that regulate DNA methylation reprogramming during early embryogenesis. In the mouse zygote, dimethylated histone H3 lysine 9 (H3K9me2) attracts Dppa3 to prevent Tet3-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here, we addressed the interplay between Dppa3 and Tet3 or H3K9me2 in somatic cells. In mouse NIH3T3 cells, the exogenously expressed Dppa3 preferentially accumulated in the cytoplasm and had no effect on Tet3-mediated 5hmC generation. In HeLa cells, the expressed Dppa3 was predominantly localised in the nucleus and could partially suppress Tet3-induced 5hmC accumulation, but this suppressive function was not correlated with H3K9me2. Co-immunoprecipitation assays further revealed an interaction of Dppa3 with Tet3 but not with H3K9me2 in HeLa cells. In cloned zygotes from somatic cells, Dppa3 distribution and 5hmC accumulation in nuclei were not affected by H3K9me2 levels. Taken together, these results suggest that H3K9me2 is not functionally associated with Dppa3 and Tet3 in somatic cells or somatic cell cloned embryos.
Additional keywords: DNA demethylation, embryo, somatic cell nuclear transfer, Stella/PGC7.
References
Baas, R., Sijm, A., Teeffelen, H. A. A. M. V., Es, R. V., Vos, H. R., and Timmers, H. T. M. (2016). Quantitative proteomics of the SMAD (suppressor of mothers against decapentaplegic) transcription factor family identifies importin 5 as a bone morphogenic protein receptor SMAD-specific importin. J. Biol. Chem. 291, 24121–24132.| Quantitative proteomics of the SMAD (suppressor of mothers against decapentaplegic) transcription factor family identifies importin 5 as a bone morphogenic protein receptor SMAD-specific importin.Crossref | GoogleScholarGoogle Scholar |
Bian, C., and Yu, X. (2014). PGC7 suppresses TET3 for protecting DNA methylation. Nucleic Acids Res. 42, 2893–2905.
| PGC7 suppresses TET3 for protecting DNA methylation.Crossref | GoogleScholarGoogle Scholar |
Dean, W., Santos, F., Stojkovic, M., Zakhartchenko, V., Walter, J., Wolf, E., and Reik, W. (2001). Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc. Natl. Acad. Sci. USA 98, 13734–13738.
| Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos.Crossref | GoogleScholarGoogle Scholar |
Deane, R., Schäfer, W., Zimmermann, H. P., Mueller, L., Görlich, D., Prehn, S., Ponstingl, H., and Bischoff, F. R. (1997). Ran-binding protein 5 (RanBP5) is related to the nuclear transport factor importin-beta but interacts differently with RanBP1. Mol. Cell. Biol. 17, 5087–5096.
| Ran-binding protein 5 (RanBP5) is related to the nuclear transport factor importin-beta but interacts differently with RanBP1.Crossref | GoogleScholarGoogle Scholar |
Funaki, S., Nakamura, T., Nakatani, T., Umehara, H., Nakashima, H., and Nakano, T. (2014). Inhibition of maintenance DNA methylation by Stella. Biochem. Biophys. Res. Commun. 453, 455–460.
| Inhibition of maintenance DNA methylation by Stella.Crossref | GoogleScholarGoogle Scholar |
Funaki, S., Nakamura, T., Nakatani, T., Umehara, H., Nakashima, H., Okumura, M., Oboki, K., Matsumoto, K., Saito, H., and Nakano, T. (2015). Global DNA hypomethylation coupled to cellular transformation and metastatic ability. FEBS Lett. 589, 4053–4060.
| Global DNA hypomethylation coupled to cellular transformation and metastatic ability.Crossref | GoogleScholarGoogle Scholar |
Gu, T. P., Guo, F., Yang, H., Wu, H. P., Xu, G. F., Liu, W., Xie, Z. G., Shi, L., He, X., Jin, S. G., Iqbal, K., Shi, Y. G., Deng, Z., Szabo, P. E., Pfeifer, G. P., Li, J., and Xu, G. L. (2011). The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606–610.
| The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes.Crossref | GoogleScholarGoogle Scholar |
He, Y. F., Li, B. Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L., Sun, Y., Li, X., Dai, Q., Song, C. X., Zhang, K., He, C., and Xu, G. L. (2011). Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307.
| Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA.Crossref | GoogleScholarGoogle Scholar |
Huang, Y., Kim, J. K., Do, D. V., Lee, C., Penfold, C. A., Zylicz, J. J., Marioni, J. C., Hackett, J. A., and Surani, M. A. (2017). Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition. eLife 6, e22345.
| Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.Crossref | GoogleScholarGoogle Scholar |
Iqbal, K., Jin, S. G., Pfeifer, G. P., and Szabó, P. E. (2011). Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. USA 108, 3642–3647.
| Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine.Crossref | GoogleScholarGoogle Scholar |
Ito, S., D’Alessio, A. C., Taranova, O. V., Hong, K., Sowers, L. C., and Zhang, Y. (2010). Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133.
| Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification.Crossref | GoogleScholarGoogle Scholar |
Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., and Zhang, Y. (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303.
| Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.Crossref | GoogleScholarGoogle Scholar |
Kikyo, N., Wade, P. A., Guschin, D., Ge, H., and Wolffe, A. P. (2000). Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI. Science 289, 2360–2362.
| Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI.Crossref | GoogleScholarGoogle Scholar |
Liu, H., Zhang, L., Wei, Q., Shi, Z., Shi, X., Du, J., Huang, C., Zhang, Y., and Guo, Z. (2017). Comprehensive proteomic analysis of PGC7-interacting proteins. J. Proteome Res. 16, 3113–3123.
| Comprehensive proteomic analysis of PGC7-interacting proteins.Crossref | GoogleScholarGoogle Scholar |
Maiti, A., and Drohat, A. C. (2011). Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem. 286, 35334–35338.
| Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites.Crossref | GoogleScholarGoogle Scholar |
Maki, N., Suetsugu-Maki, R., Sano, S., Nakamura, K., Nishimura, O., Tarui, H., Del Rio-Tsonis, K., Ohsumi, K., Agata, K., and Tsonis, P. A. (2010). Oocyte-type linker histone B4 is required for transdifferentiation of somatic cells in vivo. FASEB J. 24, 3462–3467.
| Oocyte-type linker histone B4 is required for transdifferentiation of somatic cells in vivo.Crossref | GoogleScholarGoogle Scholar |
Mayer, W., Niveleau, A., Walter, J., Fundele, R., and Haaf, T. (2000). Demethylation of the zygotic paternal genome. Nature 403, 501–502.
| Demethylation of the zygotic paternal genome.Crossref | GoogleScholarGoogle Scholar |
McGrath, J., and Solter, D. (1983). Nuclear transplantation in the mouse embryo by microsurgery and cell fusion. Science 220, 1300–1302.
| Nuclear transplantation in the mouse embryo by microsurgery and cell fusion.Crossref | GoogleScholarGoogle Scholar |
Nakamura, T., Arai, Y., Umehara, H., Masuhara, M., Kimura, T., Taniguchi, H., Sekimoto, T., Ikawa, M., Yoneda, Y., Okabe, M., Tanaka, S., Shiota, K., and Nakano, T. (2007). PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat. Cell Biol. 9, 64–71.
| PGC7/Stella protects against DNA demethylation in early embryogenesis.Crossref | GoogleScholarGoogle Scholar |
Nakamura, T., Liu, Y. J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., and Nakano, T. (2012). PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature 486, 415–419.
| PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos.Crossref | GoogleScholarGoogle Scholar |
Nakashima, H., Kimura, T., Kaga, Y., Nakatani, T., Seki, Y., Nakamura, T., and Nakano, T. (2013). Effects of Dppa3 on DNA methylation dynamics during primordial germ cell development in mice. Biol. Reprod. 88, 125.
| Effects of Dppa3 on DNA methylation dynamics during primordial germ cell development in mice.Crossref | GoogleScholarGoogle Scholar |
Nakatani, T., Yamagata, K., Kimura, T., Oda, M., Nakashima, H., Hori, M., Sekita, Y., Arakawa, T., Nakamura, T., and Nakano, T. (2015). Stella preserves maternal chromosome integrity by inhibiting 5hmC-induced gammaH2AX accumulation. EMBO Rep. 16, 582–589.
| Stella preserves maternal chromosome integrity by inhibiting 5hmC-induced gammaH2AX accumulation.Crossref | GoogleScholarGoogle Scholar |
Oswald, J., Engemann, S., Lane, N., Mayer, W., Olek, A., Fundele, R., Dean, W., Reik, W., and Walter, J. (2000). Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478.
| Active demethylation of the paternal genome in the mouse zygote.Crossref | GoogleScholarGoogle Scholar |
Payer, B., Saitou, M., Barton, S. C., Thresher, R., Dixon, J. P. C., Zahn, D., Colledge, W. H., Carlton, M. B. L., Nakano, T., and Surani, M. A. (2003). Stella is a maternal effect gene required for normal early development in mice. Curr. Biol. 13, 2110–2117.
| Stella is a maternal effect gene required for normal early development in mice.Crossref | GoogleScholarGoogle Scholar |
Saitou, M., Barton, S. C., and Surani, M. A. (2002). A molecular programme for the specification of germ cell fate in mice. Nature 418, 293–300.
| A molecular programme for the specification of germ cell fate in mice.Crossref | GoogleScholarGoogle Scholar |
Santos, F., Zakhartchenko, V., Stojkovic, M., Peters, A., Jenuwein, T., Wolf, E., Reik, W., and Dean, W. (2003). Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos. Curr. Biol. 13, 1116–1121.
| Epigenetic marking correlates with developmental potential in cloned bovine preimplantation embryos.Crossref | GoogleScholarGoogle Scholar |
Shin, S. W., John Vogt, E., Jimenez-Movilla, M., Baibakov, B., and Dean, J. (2017). Cytoplasmic cleavage of DPPA3 is required for intracellular trafficking and cleavage-stage development in mice. Nat. Commun. 8, 1643–1654.
| Cytoplasmic cleavage of DPPA3 is required for intracellular trafficking and cleavage-stage development in mice.Crossref | GoogleScholarGoogle Scholar |
Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., and Rao, A. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935.
| Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.Crossref | GoogleScholarGoogle Scholar |
Teranishi, T., Tanaka, M., Kimoto, S., Ono, Y., Miyakoshi, K., Kono, T., and Yoshimura, Y. (2004). Rapid replacement of somatic linker histones with the oocyte-specific linker histone H1foo in nuclear transfer. Dev. Biol. 266, 76–86.
| Rapid replacement of somatic linker histones with the oocyte-specific linker histone H1foo in nuclear transfer.Crossref | GoogleScholarGoogle Scholar |
Wang, L., Teng, F., Yuan, X., Liu, C., Wang, J., Li, Y., Cui, T., Li, T., Liu, Z., and Zhou, Q. (2017). Overexpression of Stella improves the efficiency of nuclear transfer reprogramming. J. Genet. Genomics 44, 363–366.
| Overexpression of Stella improves the efficiency of nuclear transfer reprogramming.Crossref | GoogleScholarGoogle Scholar |
Wossidlo, M., Nakamura, T., Lepikhov, K., Marques, C. J., Zakhartchenko, V., Boiani, M., Arand, J., Nakano, T., Reik, W., and Walter, J. (2011). 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2, 241–248.
| 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming.Crossref | GoogleScholarGoogle Scholar |
Xu, X., Pantakani, D. V., Luhrig, S., Tan, X., Khromov, T., Nolte, J., Dressel, R., Zechner, U., and Engel, W. (2011). Stage-specific germ-cell marker genes are expressed in all mouse pluripotent cell types and emerge early during induced pluripotency. PLoS One 6, e22413.
| Stage-specific germ-cell marker genes are expressed in all mouse pluripotent cell types and emerge early during induced pluripotency.Crossref | GoogleScholarGoogle Scholar |
Xu, X., Smorag, L., Nakamura, T., Kimura, T., Dressel, R., Fitzner, A., Tan, X., Linke, M., Zechner, U., Engel, W., and Pantakani, D. V. (2015). Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting. Nat. Commun. 6, 6008–6018.
| Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting.Crossref | GoogleScholarGoogle Scholar |
Yuda, A., Lee, W. S., Petrovic, P., and Mcculloch, C. A. (2018). Novel proteins that regulate cell extension formation in fibroblasts. Exp. Cell Res. 365, 85–96.
| Novel proteins that regulate cell extension formation in fibroblasts.Crossref | GoogleScholarGoogle Scholar |