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escape postfertilization reprogramming of DNA methylation, and evidence
also indicates that some nonimprinted genes and methylated CpG islands are
incompletely demethylated or retain parental methylation patterns (
Borgel
et al., 2010
).
Xenopus
embryos also maintain a high methylation level
(
Bogdanovic et al., 2011
). Therefore, some sperm DNA methylation pat-
terns are retained after fertilization, and the “methylation fate” of specific
genes or genomic sequences appears to be diverse in the early embryo.
As in mammals, zebrafish undergoes global demethylation and
remethylation after fertilization (
Mhanni & McGowan, 2004
;
Fig. 3.2
C).
Zebrafish sperm is hypermethylated relative to the oocyte (this does not, how-
ever, mean that the entire sperm genome is methylated; see below), and fol-
lowing postfertilization demethylation and remethylation, DNA methylation
levels in the embryo are similar to those of somatic tissues (
Mhanni &
McGowan, 2004; Rai et al., 2008; Wu, Zhang, Hammoud, et al., 2011
;
Fig. 3.2
C). To refine global embryonic methylation patterns, we have
recently examined changes in methylation of the promoter of all RefSeq
zebrafish genes using a methylated DNA immunoprecipitation (MeDIP)
approach coupled to hybridization of the precipitated DNA to promoter
arrays (
Andersen, Reiner, et al., 2012
). Nearly 4000 genes are methylated
at the 256-cell stage (i.e., pre-MBT, two cell cycles before ZGA) and an addi-
tional 2000 are methylated at the MBT (
Fig. 3.2
D). The number of methyl-
ated genes remains similar after the MBT (4.5-h postfertilization), yet distinct
subsets of genes are demethylated and methylated after MBT (
Fig. 3.2
D).
Thus, the transition through the MBT period is accompanied by dynamic
changes in promoter DNA methylation, albeit for a relatively minor propor-
tion of genes (2000/12,697 RefSeq genes). For the most part, promoters
retain either a methylated or unmethylated state throughout pre-MBT devel-
opment and through the MBT (
Andersen, Reiner, et al., 2012
). This suggests
that in zebrafish, as in
Xenopus
embryos (
Bogdanovic et al., 2011
), DNA
methylation patterns on upstream regulatory regions seem to be uncoupled
from gene expression changes taking place at the time of ZGA.
Several developmental features nevertheless arise from promoter DNA
methylation patterns before, during, and after ZGA. In particular, develop-
ment through the MBT period is associated with differential methylation of
low and high CpG content promoters, with preferential methylation of high
CpG promoters (
Andersen, Reiner, et al., 2012
). This suggests that devel-
opmentally associated CpG-rich promoters, including CpG islands, are not
as strongly protected from
de novo
methylation in embryonic cells as in dif-
ferentiated cells, in which they are more resilient to
de novo
methylation.
