Biology Reference
In-Depth Information
patterns of vertebrate gene methylation having been comparatively stable over
relatively long periods of evolutionary time.
The CpG dinucleotide as a mutation hotspot.
CpG has been found to be a
hotspot for mutation in a wide range of different human genes (reviewed by
Cooper and Krawczak, 1993). Of the single base-pair substitutions so far
reported to cause human genetic disease (Krawczak
et al
., 1998), ~30% involve a
CpG dinucleotide, and ~79% (~23% of the total) of these are either C
T or
G
A transitions. These data imply that the rate at which CpG mutates to either
TpG or CpA is some five-fold higher than the basal mutation rate per nucleotide.
Methylation-mediated deamination of 5mC therefore represents a major cause of
gene mutability leading to human genetic disease.
The proportion of human gene mutations compatible with a model of methyla-
tion-mediated deamination (CG
TG, CA) is however very much an average fig-
ure and provides no information on individual genes. When these values are
recalculated on a gene-specific basis, considerable variation becomes apparent.
The frequency of CG
CA mutations may be smaller than 10%
(
HBB
(4%),
HPRT1
(5%),
TTR
(9%)) or larger than 50% (
MYH7
(67%),
ADA
(63%),
RB1
(57%)). In the assumed absence of a detection bias (Cooper and
Krawczak, 1993), we may surmise that this variation is due either to differences in
(a) germline DNA methylation and/or (b) relative intragenic CpG frequency
(itself dependent upon (a)). Imbalances in the propensity to transition at CpG
dinucleotides exist even between the two DNA strands. For the human hypoxan-
thine phosphoribosyltransferase (
HPRT1
) gene, Skandalis
et al
. (1994) have
noted a significant strand bias in mutations recovered at CpG sites, thereby con-
firming our own findings (Cooper and Krawczak, 1993; Krawczak
et al
., 1998).
CpG hypermutability in inherited disease implies that the CpG sites in ques-
tion are methylated in the germline thereby rendering them prone to 5mC deam-
ination. However, on its own, CpG hypermutability still represents very indirect
evidence for CpG methylation. That 5mC deamination is itself directly responsi-
ble for these mutational events is evidenced by the fact that several cytosine
residues known to have undergone a germline mutation in the low density
lipoprotein receptor (
LDLR
; hypercholesterolemia), p53 (
TP53
; various types of
tumor), factor VIII (
F8C
; hemophilia A), and neurofibromatosis type 1 (
NF1
)
genes are indeed methylated in sperm (Rideout
et al
., 1990; Andrews
et al
., 1996;
Millar
et al
., 1998; El-Maarri
et al
., 1998). As yet, however, these are the only stud-
ies to have attempted to correlate CpG hypermutability with DNA methylation
directly for specific CpG dinucleotides.
TG and CG
Imprinting and imprinted genes.
DNA methylation is thought to be involved
in
imprinting
which was defined by Monk (1988) as the 'differential modification
of the maternal and paternal contributions to the zygote, resulting in the differ-
ential expression of parental alleles during development and in the adult.' This
differential modification appears to be essential for normal mammalian develop-
ment since parthenogenetic embryos (whether diploid paternal or diploid mater-
nal) do not survive to term: in diploid maternal embryos, fetal development is
normal but development of the extraembryonic membranes is abnormal. In
