The CpG sites or CG sites are regions of DNA where a cytosine nucleotide occurs
next to a guanine nucleotide in the linear sequence of bases along its
length. "CpG" is shorthand for "—C—phosphate—G—", that is, cytosine and
guanine separated by only one phosphate; phosphate links any two nucleosides
together in DNA. The "CpG" notation is used to distinguish this linear sequence
from the CG base-pairing of cytosine and guanine. The CpG notation can also be
interpreted as the cytosine being 5 prime to the guanine base.
Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. In
mammals, methylating the cytosine within a gene can change its expression, a
mechanism that is part of a larger field of science studying gene regulation that
is called epigenetics. Enzymes that add a methyl group are called DNA
methyltransferases. In mammals, 70% to 80% of CpG cytosines
are methylated. Unmethylated CpG dinucleotide sites can
be detected by Toll-like receptor 9 on plasmacytoid dendritic cells, monocytes,
natural killer cells, and B cells in humans. This is used to detect
intracellular viral, fungal, and bacterial pathogen DNA.
Frequency in vertebrates CpG dinucleotides have long been
observed to occur with a much lower frequency in the sequence of vertebrate
genomes than would be expected due to random chance. For example, in the human
genome, which has a 42% GC content, a pair of nucleotides consisting of
cytosine followed by guanine would be expected to occur 0.21 * 0.21 = 4.41% of
the time. The frequency of CpG dinucleotides in human genomes is 1% —
less than one-quarter of the expected frequency. Scarano et al. proposed that
the CpG deficiency is due to an increased vulnerability of
methylcytosines to spontaneously deaminate to thymine in genomes with CpG
cytosine methylation. CpG islands
CpG islands are regions with a high frequency of CpG sites, though objective
definitions for CpG islands are limited. The usual formal definition of a CpG
island is a region with at least 200 bp, and a GC percentage that is greater than
50 %, and with an observed-to-expected CpG ratio that is greater than 60 %. The
"observed-to-expected CpG ratio" can be derived where the observed is calculated
as: and the expected as:
or Many genes in mammalian genomes have CpG
islands associated with the start of the gene. Because of this, the presence of a
CpG island is used to help in the prediction and annotation of genes.
In mammalian genomes, CpG islands are typically 300-3,000 base pairs in
length, and have been found in or near approximately 40% of promoters of
mammalian genes. About 70% of human promoters have a high CpG content. Given
the frequency of GC two-nucleotide sequences, the number of CpG
dinucleotides is much lower than would be expected.
A 2002 study revised the rules of CpG island prediction to exclude other
GC-rich genomic sequences such as Alu repeats. Based on an extensive search on
the complete sequences of human chromosomes 21 and 22, DNA regions
greater than 500 bp were found more likely to be the "true" CpG islands
associated with the 5' regions of genes if they had a GC content greater than
55%, and an observed-to-expected CpG ratio of 65%.
CpG islands are characterized by CpG dinucleotide content of at least 60% of
that which would be statistically expected, whereas the rest of the genome
has much lower CpG frequency, a phenomenon called CG suppression. Unlike
CpG sites in the coding region of a gene, in most instances the CpG sites in
the CpG islands of promoters are unmethylated if the genes are expressed.
This observation led to the speculation that methylation of CpG sites in the
promoter of a gene may inhibit gene expression. Methylation, along with
histone modification, is central to imprinting. Most of the methylation
differences between tissues, or between normal and cancer samples, occur a short
distance from the CpG islands rather than in the islands themselves.
CpG islands typically occur at or near the transcription start site of genes,
particularly housekeeping genes, in vertebrates. A C base followed
immediately by a G base is rare in vertebrate DNA because the cytosines in
such an arrangement tend to be methylated. This methylation helps
distinguish the newly synthesized DNA strand from the parent strand, which
aids in the final stages of DNA proofreading after duplication. However,
over time methylated cytosines tend to turn into thymines because of
spontaneous deamination. There is a special enzyme in humans that
specifically replaces T's from T/G mismatches. However, due to the rarity
of CpGs, it is theorised to be insufficiently effective in preventing a
possibly rapid mutation of the dinucleotides. The existence of CpG
islands is usually explained by the existence of selective forces for
relatively high CpG content, or low levels of methylation in that genomic
area, perhaps having to do with the regulation of gene expression. Recently
a study showed that most CpG islands are a result of non-selective forces.
Methylation, silencing, cancer, and aging
Methylation of CpG sites within the promoters of genes can lead to their
silencing, a feature found in a number of human cancers. In contrast, the
hypomethylation of CpG sites has been associated with the over-expression of
oncogenes within cancer cells. Since age has a strong effect on DNA
methylation levels on tens of thousands of CpG sites, one can define a highly
accurate biological clock in humans and chimpanzees.
See also TLR9, detector of unmethylated CpG sites
DNA methylation age References