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

Seisenberger S, Peat JR, Hore TA, Santos F, Dean W, Reik W - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK. stefanie.seisenberger@babraham.ac.uk

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.

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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.
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RSTB20110330F2: 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.

Mentions: Recent advances have begun to elucidate how such dramatic demethylation in the zygote and PGCs is orchestrated, but a clear picture of the mechanistic details of this reprogramming and its consequences has not yet emerged. DNA methylation can be lost either through ‘passive’ dilution owing to a lack of maintenance at replication, or by ‘active’ enzyme-catalysed removal of 5mC from the DNA (figure 2). A direct DNA demethylase that is capable of cleaving the carbon–carbon bond between the methyl-group and the deoxyribose of the cytosine (C) has not been identified in mammals, but recent work has explored indirect demethylation pathways that involve deamination or oxidation of 5mC potentially coupled with base excision repair (BER; figure 2). Deamination of 5mC and C by the deaminases AID and APOBEC1 can initiate BER pathways, including potentially the glycosylases TDG and MBD4 as well as the DNA damage response protein GADD45 [5]. Oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and further to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) can have two consequences: it can abolish the generally repressive effect of the original 5mC and it can be replaced by unmodified cytosine through various routes potentially, including DNA replication, deamination and BER [6]. Research using new mouse models targeting these putative demethylation pathways has provided evidence for their involvement in germline reprogramming [7–9]. In addition, cell-culture paradigms representing different stages of the germline have recently been developed, and study of how these models—which vary in their developmental potency—may be interconverted has proved fruitful in uncovering the significance of DNA methylation reprogramming. Here, we review novel insights into how DNA methylation is reprogrammed in the mouse germline and speculate on its purpose.Figure 2.


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

Seisenberger S, Peat JR, Hore TA, Santos F, Dean W, Reik W - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2013)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539359&req=5

RSTB20110330F2: 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.
Mentions: Recent advances have begun to elucidate how such dramatic demethylation in the zygote and PGCs is orchestrated, but a clear picture of the mechanistic details of this reprogramming and its consequences has not yet emerged. DNA methylation can be lost either through ‘passive’ dilution owing to a lack of maintenance at replication, or by ‘active’ enzyme-catalysed removal of 5mC from the DNA (figure 2). A direct DNA demethylase that is capable of cleaving the carbon–carbon bond between the methyl-group and the deoxyribose of the cytosine (C) has not been identified in mammals, but recent work has explored indirect demethylation pathways that involve deamination or oxidation of 5mC potentially coupled with base excision repair (BER; figure 2). Deamination of 5mC and C by the deaminases AID and APOBEC1 can initiate BER pathways, including potentially the glycosylases TDG and MBD4 as well as the DNA damage response protein GADD45 [5]. Oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and further to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) can have two consequences: it can abolish the generally repressive effect of the original 5mC and it can be replaced by unmodified cytosine through various routes potentially, including DNA replication, deamination and BER [6]. Research using new mouse models targeting these putative demethylation pathways has provided evidence for their involvement in germline reprogramming [7–9]. In addition, cell-culture paradigms representing different stages of the germline have recently been developed, and study of how these models—which vary in their developmental potency—may be interconverted has proved fruitful in uncovering the significance of DNA methylation reprogramming. Here, we review novel insights into how DNA methylation is reprogrammed in the mouse germline and speculate on its purpose.Figure 2.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK. stefanie.seisenberger@babraham.ac.uk

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.

Show MeSH