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as a signature of replication-dependent loss of DNA methylation (
Rougier
et al., 1998
). More recent genome-wide molecular studies confirmed a
gradual decrease in both CG and non-CGmethylation toward implantation,
reaching a minimal level by E3.5 (embryonic day 3.5 postfertilization)
blastocysts, for both oocyte- and sperm-specific gDMRs (
Smith et al.,
2012
). However, while this phenomenon is prominent at repeated
sequences, a significant proportion of CpG-rich CGI sequences are resistant
to DNA demethylation. In particular, 20-60% of oocyte-methylated CGIs
maintain methylation in the blastocyst, which represent a variable estimation
between 200 and 800 loci, depending on studies (
Table 9.1
;
Kobayashi et al.,
2012; Smallwood et al., 2011
). As discussed earlier, fewer sperm-specific
gDMRs exist as CGIs and about 35 paternal CGIs are maintained from
sperm to blastocysts. These numbers indicate that protection of parent-
specific methylation extends beyond the 23 known ICRs.
Key molecular players responsible for the maintenance and protection of
specific loci against passive demethylation have recently been identified. The
Kr¨ppel-associated box-containing zinc-finger protein ZFP57 was the first
component shown to be involved in maintenance of ICR methylation dur-
ing early embryonic development (
Li et al., 2008
). ZFP57 enables DNA
binding of a heterochromatin protein complex organized around KAP1
(Kr¨ppel-associated protein, also known as TRIM28), which also contains
the H3K9 methyltransferase SETB1, HP1, and the nucleosome remodeling
NuRD complex. Accordingly, loss of maternally inherited KAP1 also results
in stochastic loss of DNA methylation at known maternal and paternal ICRs
as well as embryonic lethality at midgestation (
Li et al., 2008; Messerschmidt
et al., 2012
). In ES cells, KAP1 partners include the different DNA met-
hyltransferases, DNMT1, DNMT3A, and DNMT3B (
Quenneville et al.,
2011; Zuo et al., 2012
). KAP1 could therefore promote sequence-specific
conservation of DNA methylation during cell divisions either by targeting
DNMT1 maintenance activity or by targeting reiterative
de novo
methyla-
tion via DNMT3A and DNMT3B at these loci.
Two recent ChIP-Seq studies in ES cells describe binding sites for the
KAP1 maintenance complex genome wide (
Quenneville et al., 2011;
Zuo et al., 2012
). Three members of the KAP1 repressive complex
(ZFP57, KAP1, and SETDB1) colocalize at 91 discrete loci, including all
known ICRs. ZFP57 was moreover shown to be required for proper
KAP1 binding and maintenance of DNA methylation at these loci
(
Quenneville et al., 2011
). Sequence analysis of ZFP57 binding sites rev-
ealed (TGCCGC) hexameric motifs, which can only be bound by
