Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers

Abstract

In mammalian development, epigenetic modifications, including DNA methylation patterns, play a crucial role in defining cell fate but also represent epigenetic barriers that restrict developmental potential. At two points in the life cycle, DNA methylation marks are reprogrammed on a global scale, concomitant with restoration of developmental potency. DNA methylation patterns are subsequently re-established with the commitment towards a distinct cell fate. This reprogramming of DNA methylation takes place firstly on fertilization in the zygote, and secondly in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. In each reprogramming window, a unique set of mechanisms regulates DNA methylation erasure and re-establishment. Recent advances have uncovered roles for the TET3 hydroxylase and passive demethylation, together with base excision repair (BER) and the elongator complex, in methylation erasure from the zygote. Deamination by AID, BER and passive demethylation have been implicated in reprogramming in PGCs, but the process in its entirety is still poorly understood. In this review, we discuss the dynamics of DNA methylation reprogramming in PGCs and the zygote, the mechanisms involved and the biological significance of these events. Advances in our understanding of such natural epigenetic reprogramming are beginning to aid enhancement of experimental reprogramming in which the role of potential mechanisms can be investigated in vitro. Conversely, insights into in vitro reprogramming techniques may aid our understanding of epigenetic reprogramming in the germline and supply important clues in reprogramming for therapies in regenerative medicine.

Figure 1.

DNA methylation reprogramming in the mammalian life cycle. DNA methylation marks represent an epigenetic barrier in mammalian development that is demolished when developmental potency has to be restored and subsequently re-built with the commitment to a particular cell fate. This first occurs following fertilization, when the DNA methylation marks of the parental gametes are erased in two waves of demethylation. In the first wave, the paternal pronucleus (shown in blue) undergoes rapid demethylation in the zygote, which is followed by a passive loss of DNA methylation marks in the maternal genome (shown in red) over the subsequent cell divisions. Re-establishment of DNA methylation marks commences in the ICM of the developing embryo, which forms an epigenetic barrier (dashed line) in the developmentally more restricted epiblast. PGCs (shown in green) inherit the epigenetic signature from the epiblast, and DNA methylation is again erased on a global scale concomitant with the restoration of developmental potency. Note that DNA methylation at DMRs of imprinted genes become reset in PGCs but are protected from reprogramming in the early embryo. With further development into fully specialized gametes, DNA methylation marks are re-established and developmental potency is restricted. This epigenetic barrier (dashed line) will be demolished once more in the zygote of the next generation as part of the continuous cycle of DNA methylation reprogramming.

Figure 2.

Pathways for removal of DNA methylation. Cytosine (C) is methylated at the 5′ carbon position by DNMT enzymes to generate 5-methylcytosine (5mC). This can be lost passively owing to a lack of maintenance at DNA replication (dashed line), or actively processed by enzymatic activity. 5mC can be deaminated to thymine (T) by the AID/APOBEC deaminases (blue), or oxidized to 5-hydroxymethylcytosine (5hmC) by the TET enzyme family (brown). 5hmC itself may be deaminated to 5-hydroxymethyluracil (5hmC), or further oxidized by TET activity to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The T, 5hmU, 5fC and 5caC derivatives can be excised by glycosylases (beige) such as TDG, single strand-selective monofunctional uracil DNA glycosylase 1 (SMUG1) and methyl-CpG-binding domain protein 4 (MBD4) to initiate the BER pathway resulting in their replacement with unmodified C. Alternatively, 5fC and 5caC can be lost passively through lack of maintenance; 5caC may also be converted to C by a decarboxylation reaction. For clarity, demethylation catalysed by the elongator complex is not shown.