Functions of DNA Methylation and Hydroxymethylation in Mammalian Development - Current Topics in Developmental Biology - page 56

exceptions of methylated CpG island promoters, for example, at imprinted
and pluripotency-related genes, which in this case is associated with long-
term transcription silencing (see Section 4.2 ). What are the mechanisms that
exclude DNA methylation from CpG islands? There are probably multiple
factors which are not mutually exclusive ( Deaton & Bird, 2011 ). One factor
is the underlying DNA sequence, as illustrated by the fact that 1-kb pro-
moter fragments recapitulate the DNA methylation pattern of the endoge-
nous sequence when inserted somewhere else in the genome of mouse ES
cells ( Lienert et al., 2011 ). This shows that the local DNA sequence is key in
determining hypo- or hypermethylation states. This can be mediated by
transcription factors like SP1 that bind to sequence motifs in CpG islands
and have a protective effect against DNA methylation ( Brandeis et al.,
1994; Macleod, Charlton, Mullins, & Bird, 1994 ), either because they create
steric hindrance or because transcription itself inhibits DNA methylation.
Another possibility is that the particular epigenetic state of CpG islands is
mediated by CXXC proteins that bind unmethylated CpG-rich DNA.
One candidate is CXXC finger protein 1 (CFP1), a protein that is part of
the mammalian SET1 H3K4 methyltransferase complex. CFP1 binds to
unmethylated CpG islands and recruits methylation of the lysine 4 of histone
H3 (H3K4) ( Thomson et al., 2010 ), which is found at all CpG islands
irrespective of transcription ( Meissner et al., 2008; Weber et al., 2007 ).
As methylation of H3K4 has been proposed to inhibit the recruitment of
DNMTs to chromatin ( Ooi et al., 2007; Zhang, Jurkowska, et al., 2010 ),
it was tempting to speculate that CFP1-dependent H3K4 methylation pro-
tects CpG islands from DNA methylation. However, depletion of CFP1
alone is not sufficient to increase DNA methylation at CpG islands in ES
cells, suggesting that other factors cooperate with H3K4 methylation
( Clouaire et al., 2012 ). Other CXXC proteins could contribute to the
unmethylated state of CpG islands, such as TET1 (as discussed in
Section 2.2 ) or KDM2A. KDM2A binds to CpG islands and removes
H3K36me2 ( Blackledge et al., 2010 ), which could contribute to exclude
the DNA methylation machinery given that DNMT3A recognizes methyl-
ated H3K36 ( Dhayalan et al., 2010 ). Another aspect that deserves attention
is the interplay between DNA methylation and nucleosome occupancy
( Chodavarapu et al., 2010 ). In mammalian cells, unmethylated CpG islands
are relatively nucleosome free ( Fenouil et al., 2012; Kelly et al., 2012 ),
which could render them refractory to the DNA methylation machinery
because most of the cellular content of DNMT3A/B is associated with
nucleosomes ( Gowher, Stockdale, et al., 2005; Jeong et al., 2009 ). This