The tendency to recreate ancestral CG dinucleotides in the human genome

The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG din...

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Published inBMC evolutionary biology Vol. 11; no. 1; p. 3
Main Authors Li, Mingkun, Chen, Su-Shing
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 05.01.2011
BioMed Central
BMC
Subjects
Analysis
Animals
Cytosine
Deoxyribonucleic acid
Dinucleotide Repeats
DNA
DNA Methylation
Evolution, Molecular
GC Rich Sequence
Gene Frequency
Genetic aspects
Genetics
Genome, Human
Genomics
Guanine
Human genome
Humans
Mammals - classification
Mammals - genetics
Methylation
Molecular Sequence Data
Mutation
Nucleotides
Phylogeny
Physiological aspects
Polymorphism, Single Nucleotide
China
Germany
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Summary:The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutation rate destroying CG dinucleotides, vs. functional processes that require their preservation remains an unsolved question. By analyzing the mutation and frequency spectrum of newly derived alleles in the human genome, a tendency towards generating more CGs was observed, which was mainly contributed by an excess number of mutations from CA/TG to CG. Simultaneously, we found a fixation preference for CGs derived from TG/CA rather than CGs generated by other dinucleotides. These tendencies were observed both in intergenic and genic regions. An analysis of Integrated Extended Haplotype Homozygosity provided no evidence of selection for newly derived CGs. Ancestral CG dinucleotides that were subsequently lost by mutation tend to be recreated in the human genome, as indicated by a biased mutation and fixation pattern favoring new CGs that derived from TG/CA.
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ISSN:1471-2148
1471-2148
DOI:10.1186/1471-2148-11-3