Review Article | Published:

DNA methylation: roles in mammalian development

Nature Reviews Genetics volume 14, pages 204220 (2013) | Download Citation

Abstract

DNA methylation is among the best studied epigenetic modifications and is essential to mammalian development. Although the methylation status of most CpG dinucleotides in the genome is stably propagated through mitosis, improvements to methods for measuring methylation have identified numerous regions in which it is dynamically regulated. In this Review, we discuss key concepts in the function of DNA methylation in mammals, stemming from more than two decades of research, including many recent studies that have elucidated when and where DNA methylation has a regulatory role in the genome. We include insights from early development, embryonic stem cells and adult lineages, particularly haematopoiesis, to highlight the general features of this modification as it participates in both global and localized epigenetic regulation.

Key points

  • DNA methylation is essential for mammalian development and has notable roles in gene silencing, protection against spurious repetitive element activity, genomic stability during mitosis and parent-of-origin imprinting.

  • DNA methylation functions to coordinately silence some promoter and enhancer classes that are typified by low overall CpG density. By contrast, many CpG islands, particularly those at promoters, remain generally and constitutively protected from DNA methylation through numerous opposing cis- and trans-based mechanisms.

  • Embryonic stem cells (ESCs) remain one of the most highly studied in vitro models for dissecting epigenetic mechanisms during cellular differentiation. They are unique in their ability to retain the molecular characteristics of their cellular state in the absence of DNA methylation but cannot differentiate into embryonic lineages while simultaneously gaining extra-embryonic potential.

  • ESCs are also unique in their heterogeneous ability to maintain repetitive element silencing through DNA methyltransferase 1 (DNMT1) maintenance activity alone and rely on the DNMT3 enzymes to re-silence these elements continuously de novo. The pre-implantation stage of development is one of the few stages at which endogeneous transposable elements are actively regulated.

  • Promoters of germline-specific genes are coordinately repressed by DNMT3B in embryonic lineages and are reactivated during the global demethylation that accompanies primordial germ cell (PGC) specification.

  • Haematopoiesis has served as a benchmark model for the function of DNA methylation in adult stem cells and in later lineage specification. Several notable regulatory principles for DNA methylation were originally or comprehensively described in this system, including the gating of lymphoid versus myeloid fates, the dynamics of intragenic CpG island methylation in transcript selection and demethylation as a lineage stabilizer by providing a mitotically heritable memory of transcription factor binding.

  • DNA methylation is globally erased during specification of the germ line and during fertilization, at which point the paternal genome is specifically demethylated. These two key events have numerous related cascades of chromatin re-organization that suggest similar epigenetic mechanisms for erasure and re-establishment of global nuclear organization, although the relationship between these events remains incompletely defined.

  • Although they have remained mysterious for more than 2 decades, the targets and mechanisms for DNA methylation erasure in the paternal genome as well as for protection of the maternal genome during fertilization are becoming clearer. For example, there are distinct temporal windows for global hydroxymethylation followed by erasure to unmodified cytosines occurring later in zygotic progression. The epigenetic determinants that retain silencing at repetitive element classes and imprints are less clear, but they are likely to be discovered as the dynamics and relationships of other epigenetic regulators are refined.

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Acknowledgements

We thank members of the Meissner laboratory as well as M. M. Chan, A. Regev, T. S. Mikkelsen, R. P. Koche, H. Gu, A. Gnirke, and P. Boyle for discussion and insight. A.M. is supported by the Pew Charitable Trusts, US National Institutes of Health (NIH) grants (U01ES017155 and P01GM099117) and is a New York Stem Cell Foundation (NYSCF) Robertson Investigator.

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Affiliations

  1. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

    • Zachary D. Smith
    •  & Alexander Meissner
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

    • Zachary D. Smith
    •  & Alexander Meissner
  3. Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.

    • Zachary D. Smith
    •  & Alexander Meissner

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alexander Meissner.

Glossary

CpG islands

Regions of several hundred to approximately two thousand base pairs that are frequently found at promoters and that exhibit strong enrichment for CpG dinucleotides. Those CpG islands at promoters are predominantly unmethylated across cell types.

Symmetrically methylated CpGs

The presence of a methyl group on carbon 5 of the cytosine base is typically found on both bases within the palindromic CpGs of opposing DNA strands, reflecting successful maintenance methylation during DNA synthesis.

CXXC

A conserved Cys–X–X–Cys domain that is frequently found in developmental epigenetic regulators that bind unmethylated CpG-containing DNA and often instruct the modification of histones in ways that oppose DNA methylation.

H2A.Z

A histone H2A variant that is incorporated into euchromatic nucleosomes and is believed to contribute to the rapid exchange of histones in active genomic loci.

Azacytidine

A cytosine analogue that incorporates into synthesizing DNA and covalently binds DNA methyltransferases (DNMTs), sequestering and inhibiting their function. It is used in some cancer therapies.

TET dioxygenases

Enzymes that associate with DNA and use α-ketoglutarate and Fe2+ cofactors to mediate the oxidation of methylated cytosine to hydroxy-, formyl- or carboxymethylcytosine, which are potential demethylation intermediates.

Lymphoid-specific helicase

(LSH). A SWI/SNF-like helicase believed to participate in the remodelling of nucleosomes that is necessary to initiate heterochromatin assembly and de novo methylation.

Minor satellite

A repetitive array of AT-rich sequences that instructs the formation of the centromeric nucleosomes to form the kinetocore and to permit sister chromatid pairing. Centromere protein B (CENPB) mediates the assembly of CENPA-containing nucleosomes.

Lagging anaphase bridges

Delayed sister chromatid segregation during mitosis as a consequence of faulty centromere formation or connection to the mitotic spindle; a frequent cause of chromosome loss and aneuploidy.

Long interspersed nuclear elements

(LINEs). A type of repetitive element that encodes the necessary proteins for integration into the genome of its reverse-transcribed RNA transcript. It preferentially integrates within gene-poor regions.

Trophectodermal lineage

Cells that contribute to placental tissues. They are derived from the external component of blastocyst stage embryos; this represents the first restriction in cellular potency during mammalian development.

Intracisternal A-type particles

(IAPs). These are notable class II long terminal repeat (LTR)-containing retroelements that are specific to mice and that retain high methylation levels throughout development.

Hemimethylation

Asymmetric methylation of only one cytosine within opposing CpGs. If not remethylated during S phase by DNA methyltransferase 1 (DNMT1), hemimethylated DNA can lead to loss of mitotic inheritance after a subsequent round of replication.

Hydroxymethylation

Oxidation of the methyl group as mediated by the TET dioxygenases through α-ketoglutarate catalysis. Hydroxymethylated residues can be further oxidized to formyl- and carboxymethylcytosine.

Germline-specific genes

Genes of unique gametogenic function that are tightly regulated outside gametes or the early embryo by DNA methylation. They are specifically demethylated during primordial germ cell specification.

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DOI

https://doi.org/10.1038/nrg3354

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