Biology Reference
In-Depth Information
have an increased incidence of developmental failures and fail to properly
erase 5mC from the paternal genome in the preimplantation embryos
(see
Section 5.1
;
Gu et al., 2011
). Even though the levels of 5hmC are
the highest in the adult brain, no neurological phenotypes have so far been
reported in
Tet
-knockout mice.
3. PATTERNS OF DNA METHYLATION AND
HYDROXYMETHYLATION DURING DEVELOPMENT
3.1. Distribution of 5mC in mammalian genomes
In mammals, cytosine methylation is found almost exclusively in the context
of CpG dinucleotides. CpGs occur with a low frequency in vertebrate
genomes, that is, on average less than one quarter of the expected frequency
in the human and mouse genomes (
Fig. 2.3
A), because they are progres-
sively lost over evolutionary time by spontaneous deamination of 5mC into
thymines in the germ line. In accordance with this model, organisms with-
out DNAmethylation (such as
Drosophila melanogaster
) show no signs of CpG
depletion (
Fig. 2.3
A) and methylated sequences in sperm show higher rates
of CpG loss during primate evolution (
Molaro et al., 2011; Weber et al.,
2007
). Mammalian genomes contain only few areas with higher CpG den-
sity, termed “CpG islands,” which are typically 0.5-2-kb long and colocalize
with 60-70% of annotated gene promoters, including most housekeeping
genes and many tissue-specific genes. These CpG islands do not result from
a positive selection for CpGs but rather from a neutral effect reflecting the
fact that they are unmethylated in the germ line and therefore not prone to
CpG loss during evolution (
Cohen, Kenigsberg, & Tanay, 2011
).
In order to better define the distribution of CpG methylation, technol-
ogies have emerged to map 5mC genome wide with restriction enzymes,
affinity purification, or sodium bisulfite treatment in combination with
microarrays or high-throughput sequencing (
Laird, 2010
). The gold-
standard approach is now to perform chemical treatment with sodium
bisulfite, which converts unmethylated cytosines into uracils while leaving
methylated cytosines unchanged, followed by high-throughput sequencing
to generate quantitative methylation maps at a single-nucleotide resolution,
with the caveat that it does not discriminate between 5mC and 5hmC. The
first complete cytosine methylation maps have been generated in mouse
and human somatic cells and revealed a bimodal distribution: CpG-poor
sequences in exons, introns, and intergenic regions are heavily methylated
