DNA demethylation reprogramming in the mouse zygote
General Genetics and Functional Genome Biology
Final Report Abstract
The rapid technological progress in DNA sequencing methods in combination with further improvements and modifications of bisulfite sequencing in recent years has enabled the investigation the DNA methylation profiles just in few cells with single base resolution. This allowed us to look closely into DNA methylation/demethylation dynamics at specific sequences in carefully isolated staged PGCs and preimplantation mouse embryos. Additionally, the incorporation of 5hmC/5fC/5caC into the models, describing the DNA methylation reprogramming in developing embryos and gametes, have changed many paradigms in developmental biology and epigenetics. We demonstrated, that earlier discovered dramatic demethylation of paternal DNA in the zygote is driven by the conversion of 5mC to 5hmC (and further oxidized forms). In fact, the actual loss of modification and conversion to unmodified cytosine in pre-replicative zygotes accounts for only minor impact of active DNA demethylation. The major loss DNA modifications is replication dependent in both developing zygotes and PGCs and is characterized by the accumulation of hemi-methylated sites. Nevertheless the DNA methylation maintenance (and probably de novo methylation) is not completely impaired at DNA demethylation stages - there is still a substantial proportion of remaining fully methylated sites. The discrimination mechanisms, regulating faithful DNA methylation maintenance, still remain to be elucidated. The presence of 5mC oxidized forms drives the replication independent demethylation by either recruiting the DNA repair factors, or by interacting with DNA methylation maintenance. Normal preimplantation development requires tight regulation of Tet activity. This regulation is mediated by interactions with chromatin modifications, such as H3K9me2, and also by interactions with specific factors, such as PGC7/Stella. The dynamics of DNA and chromatin modifications in preimplantation embryos are largely conserved in different mammalian species.
Publications
- (2008). "Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes." Epigenetics & chromatin 1(1): 8
Lepikhov, K., V. Zakhartchenko, R. Hao, F. Yang, C. Wrenzycki, H. Niemann, E. Wolf and J. Walter
(See online at https://doi.org/10.1186/1756-8935-1-8) - (2009) “Effect of IVF and laser zona dissection on DNA methylation pattern of mouse zygotes”. Mammalian Genome 20(9-10): 664-673
Peters, D., Lepikhov, K., Rodenacker, K., Marschall, S., Boersma, A., Hutzler, P., Scherb, H., Walter, J. and de Angelis, M. H.
(See online at https://doi.org/10.1007/s00335-009-9227-0) - (2009). "Epigenetic modifications and related mRNA expression during bovine oocyte in vitro maturation" Reproduction, fertility, and development 21(6): 738-748
Racedo, S. E., Wrenzycki, C., Lepikhov, K., Salamone, D., Walter, J. and Niemann, H.
(See online at https://doi.org/10.1071/RD09039) - (2010). "DNA methylation reprogramming and DNA repair in the mouse zygote." Int J Dev Biol 54(11-12): 1565-1574
Lepikhov, K., M. Wossidlo, J. Arand and J. Walter
(See online at https://doi.org/10.1387/ijdb.103206kl) - (2010). "Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes." EMBO J 29(11): 1877-1888
Wossidlo, M., J. Arand, V. Sebastiano, K. Lepikhov, M. Boiani, R. Reinhardt, H. Scholer and J. Walter
(See online at https://doi.org/10.1038/emboj.2010.80) - (2011). "5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming." Nat Commun 2: 241
Wossidlo, M., T. Nakamura, K. Lepikhov, C. J. Marques, V. Zakhartchenko, M. Boiani, J. Arand, T. Nakano, W. Reik and J. Walter
(See online at https://doi.org/10.1038/ncomms1240) - (2012). "In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases." PLoS Genet 8(6): e1002750
Arand, J., D. Spieler, T. Karius, M. R. Branco, D. Meilinger, A. Meissner, T. Jenuwein, G. Xu, H. Leonhardt, V. Wolf and J. Walter
(See online at https://doi.org/10.1371/journal.pgen.1002750) - (2012). "The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells." Mol Cell 48(6): 849-862
Seisenberger, S., S. Andrews, F. Krueger, J. Arand, J. Walter, F. Santos, C. Popp, B. Thienpont, W. Dean and W. Reik
(See online at https://doi.org/10.1016/j.molcel.2012.11.001) - (2012). Epigenetic Reprogramming in Mammalian Development. Encyclopedia of Molecular Cell Biology and Molecular Medicine. R. Meyers, Wiley-VCH Verlag
Lepikhov, K., J. Arand, M. Wossidlo and J. Walter
- (2013). "Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives." Cell 152(5): 1146-59
Spruijt, C. G., F. Gnerlich, A. H. Smits, T. Pfaffeneder, P. W. Jansen, C. Bauer, M. Munzel, M. Wagner, M. Muller, F. Khan, H. C. Eberl, A. Mensinga, A. B. Brinkman, K. Lepikhov, U. Muller, J. Walter, R. Boelens, H. van Ingen, H. Leonhardt, T. Carell and M. Vermeulen
(See online at https://doi.org/10.1016/j.cell.2013.02.004) - (2013). "FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency." Cell Stem Cell 13(3): 351-359
Ficz, G., T. A. Hore, F. Santos, H. J. Lee, W. Dean, J. Arand, F. Krueger, D. Oxley, Y. L. Paul, J. Walter, S. J. Cook, S. Andrews, M. R. Branco and W. Reik
(See online at https://doi.org/10.1016/j.stem.2013.06.004) - (2013). "Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells." Cell Stem Cell 13(3): 360-369
Habibi, E., A. B. Brinkman, J. Arand, L. I. Kroeze, H. H. Kerstens, F. Matarese, K. Lepikhov, M. Gut, I. Brun-Heath, N. C. Hubner, R. Benedetti, L. Altucci, J. H. Jansen, J. Walter, I. G. Gut, H. Marks and H. G. Stunnenberg
(See online at https://doi.org/10.1016/j.stem.2013.06.002)
