DNA Methylation in Development


DNA (deoxyribonucleic acid) methylation is an epigenetic modification which can silence gene expression and stabilize repeats. A methyl group is added to cytosine when followed by guanine (CpG) and CpGs are enriched at the promoters of many genes and in retrotransposons. Nevertheless, only a small number of these CpG‐rich genes are actually regulated by methylation. These fall into three classes: imprinted genes, genes on the inactive X and germ cell‐specific genes. Methylation is reprogrammed (erased and re‐established) at two points during development: around implantation and the during germ cell development. DNA methyltransferase 3a (DNMT3A) and DNMT3B establish methylation patterns, with the help of the cofactor DNMT3L in the germ cells, then DNMT1 maintains them during mitotic division. Failure of either process leads to developmental defects, sterility or embryonic death. Histone methylation and small RNAs (ribonucleic acids) have been implicated in directing the methyltransferases to particular genes or repeats.

Key concepts:

  • DNA methylation is associated with transcriptionally inactive chromatin and helps stabilize it.

  • Methylation in mammals occurs exclusively at cytosine followed by guanine (CpG).

  • CpG‐rich regions (CpG islands) are found at the start of many genes and in retrotransposons.

  • Methylation of CpG islands maintains repression on imprinted genes, genes on the inactive X chromosome, germ cell‐specific genes and certain retrotransposons.

  • Three key enzymes are involved, DNMT1, DNMT3A and DNMT3B, together with the cofactor DNMT3L.

  • DNMT1 maintains DNA methylation on all sequences during development.

  • DNMT3A and DNMT3L are essential for imprinting and retrotransposon repression in the germ cells.

  • There is a developmental cycle of changes in the level of genomic methylation, which is necessary for the correct reprogramming of imprinted and X‐chromosome genes for the next generation.

  • Evidence is growing that histone modifications determine which DNA sequences become methylated.

Keywords: DNA methyltransferase; demethylation; germ cells; epigenetics; imprinting; CpG island

Figure 1.

The developmental methylation cycle. Methylation levels are high overall (dark shading on chromosomes) in the mature sperm and egg and they have differing patterns of methylation at paternally (blue) and maternally (pink) methylated imprinted genes, respectively. Following fertilization, methylation of the paternal genome is rapidly reduced (lighter shading), although it remains high at the imprinted genes and at some repeat sequences. Note that this takes place at a stage when paternal and maternal DNA is contained within separate pronuclei (not shown). Demethylation of the maternal genome occurs more gradually, over several cleavage divisions until the blastocyst stage. Following implantation at around E4.5, de novo methylation begins. Methylation in somatic tissues increases until birth, and changes little thereafter. Primordial germ cells (PGCs) arise at around E7.5, and show a global reduction in methylation at around E12.5, after entry into the genital ridge. This includes removal of paternally and maternally inherited methylation marks (imprint erasure). During the processes of oogenesis and spermatogenesis, methylation levels are increased once again and the appropriate sex‐specific methylation at imprinted genes is established.

Figure 2.

Targeting and maintenance of DNA methylation at an imprinted gene in the germline and the soma. A schematic diagram of the CpG island which controls expression of the imprinted maternally methylated Peg1 gene, and the factors involved in establishment and maintenance of DNA methylation at this site during mouse development. Factors involved at other genes can vary. (a) Germline. Following erasure of imprints in the PGCs, dimethylation of histone 3 lysine 4 (H3K4me2) is established (by an unidentified factor) to prevent DNA methylation. Expression of the H3K4 demethylaseKDM1B during oocyte development results in loss of H3K4me2. The germ cell‐specific cofactor DNMT3L subsequently binds to H3K4, which can only occur when H3K4 is unmethylated. Two molecules of DNMT3L form a tetramer with two subunits of DNMT3A, recruiting the latter to carry out de novo methylation of the CpG island. In the absence of any of these three proteins, methylation is not established on Peg1 in the oocytes. (b) Soma. In the zygote, only the maternally inherited allele of Peg1 is methylated, as the copy inherited from the sperm is unmethylated (not shown). As the methylated chromosome is replicated in each zygotic S phase in the pre‐implantation embryo, the daughter duplex is initially only hemimethylated and the methylation pattern must be copied onto the newly synthesized DNA strand. ZFP57 (a zinc finger protein), and PGC7/Stella (primoridal germ cell 7; protein which is expressed mainly in PGCs and immature oocytes) are required together with DNMT1 for maintenance of methylation at Peg1 and several other imprinted genes at this stage. After implantation, ZFP57 (but not PGC7/Stella) is still required and the UHRF1 protein (a PHD‐containing protein which can bind specific DNA sequences and recruit histone deacetylases) is also now needed for maintenance methylation. Together, these mechanisms ensure that one allele of Peg1 is inherited in an inactive state and remains transcriptionally silent throughout the lifetime of the organism.



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Further Reading

Aravin AA and Hannon GJ (2008) Small RNA silencing pathways in germ and stem cells. Cold Spring Harbor Symposi on Quantitative Biology 73: 283–290.

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Chow J and Heard E (2009) X inactivation and the complexities of silencing a sex chromosome. Current Opinion in Cell Biology 21: 359–366.

Niemann H, Tian XC, King WA et al. (2008) Epigenetic reprogramming in embryonic and foetal development upon somatic cell nuclear transfer cloning. Reproduction 135(2): 151–163.

Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447: 425–432.

Web Links

Epigenome Network of Excellence; Locus ID: http://www.epigenome‐noe.net/

Functional Genomics Resources: Epigenetics; Locus ID; http://www.sciencemag.org/feature/plus/sfg/resources/res_epigenetics.dtl#gen

Human Epigenome Project; Locus ID; www.epigenome.org

Lees‐Murdock D.J., Walsh, C.P. Developmental regulation of DNA methylation. Locus ID; http://www.interscience.wiley.com/mrw/eggpb

NIH Roadmap for Medical Research; Locus ID; http://nihroadmap.nih.gov/EPIGENOMICS/epigeneticmechanisms.asp

The Harwell Mouse Imprinting Site; Locus ID; http://www.har.mrc.ac.uk/research/genomic_imprinting

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Rutledge, Charlotte E, Lees‐Murdock, Diane J, and Walsh, Colum P(Apr 2010) DNA Methylation in Development. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006155.pub2]