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DNase I hypersensitive sites (
Fig. 2.3
B). At these sites, 5hmC occurs at up to
10-20% of all CpGs in the cellular population (
Yu et al., 2012
). This finding is
in agreement with other studies that also point toward a preferential
distribution of 5hmC at distal enhancers (
Serandour et al., 2012; Stroud,
Feng, Morey Kinney, Pradhan, & Jacobsen, 2011; Szulwach, Li, Li, Song,
Han, et al., 2011
); however, it is intriguing that it does not correlate with
the preferential binding of TET1 at CpG-rich sequences in ES cells (discussed
in
Section 2.2
). Interestingly, the same sequences have been identified as
LMRs in ES cells and show correspondingly lower levels of 5mC (
Stadler
et al., 2011
;
Fig. 2.3
B), suggesting that a high proportion of 5hmC is linked
with demethylation at transcription factor-binding sites. Future studies should
help to clarify whether this is a general feature in all cell types and what mech-
anisms govern the dynamics of 5mC and 5hmC at distal-regulatory regions.
3.3. Reprogramming of DNA methylation during
preimplantation development
Patterns of DNA methylation undergo drastic changes during early embry-
onic development in mammals. Early studies in mice using immunofluores-
cence and restriction enzymes revealed that DNA methylation inherited from
the gametes is globally erased after fertilization from the first cleavage stages up
to the blastocyst, before being reestablished after implantation (
Monk,
Boubelik, & Lehnert, 1987; Santos, Hendrich, Reik, & Dean, 2002
;
Fig. 2.4
). This process occurs via multiple mechanisms: the paternal DNA
undergoes rapid loss of 5mC in the zygote before the first cell division,
whereas the maternal DNA is demethylated over several cell divisions, prob-
ably as a result of lack of maintenance activity (
Saitou, Kagiwada, &Kurimoto,
2012
). There are still debates on whether the demethylation in the male pro-
nucleus also occurs with similar dynamics and amplitude in other mammals
such as sheep or rabbit (
Lepikhov et al., 2008; Reis Silva et al., 2011
). Several
groups have now overcome the difficulty to work with small amounts of cells
and applied genome-wide bisulfite sequencing to quantify the dynamics of
DNA methylation in mouse early cleavage-stage embryos (
Kobayashi et al.,
2012; Smallwood et al., 2011; Smith et al., 2012
). These studies revealed that
oocytes have a relatively hypomethylated genome compared to sperm, and
that upon fertilization methylation levels decrease to reach a low point in pre-
implantation blastocysts (
Fig. 2.4
). Even though bisulfite sequencing cannot
distinguish the kinetics of 5mC and 5hmC, these studies confirm that a major
epigenetic reprogramming event occurs after fertilization. After implantation
of the embryo, DNA methylation is progressively reestablished and is
