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PMID: 1736311 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Analysis of CpG suppression in methylated and nonmethylated species.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 89 ·No. 3 ·1992-02-01 ·Pages 957-61

Schorderet DF, Gartler SM

Abstract

The development of nearest-neighbor analysis led to the finding that the frequency of the dinucleotide CpG is markedly depressed in vertebrates. One explanation of this suppression is that methylation of CpG found in vertebrates represents a mutational hot spot through deamination of methylcytidine to thymidine. We have examined the role of methylated CpG as a factor in CpG suppression by comparing CpG distributions in coding regions of 121 genes from six species, three with methylated DNA and three with nonmethylated DNA. Overall base composition shows that all species exhibit CpG suppression, with the methylated forms showing significantly greater suppression than nonmethylated forms. When the data are analyzed by CpG position, the mean values of the methylated forms exhibit greater suppression than nonmethylated forms at positions I-II and II-III, but there is considerable overlap of suppression scores for individual species. At position III-I, CpG suppression is marked in all methylated species, and it is reversed in all nonmethylated species. Our analysis supports the hypothesis that CpG patterns at positions II-III and III-I in methylated forms are affected by mutation acting through deamination of methylcytidine to thymidine. We speculate that the excess of CpGs at position III-I in nonmethylated forms may be related to a requirement for minimal thermal stability of the DNA.

MeSH Terms
Animals Arginase/genetics Base Sequence Caenorhabditis/genetics Codon DNA/chemistry,genetics Drosophila melanogaster/genetics Genes Glyceraldehyde-3-Phosphate Dehydrogenases/genetics Humans Methylation Mice Molecular Sequence Data Phosphoglycerate Kinase/genetics Plasmodium falciparum/genetics Saccharomyces cerevisiae/genetics alpha-Amylases/genetics
Chemicals
Codon DNA Glyceraldehyde-3-Phosphate Dehydrogenases Phosphoglycerate Kinase alpha-Amylases Arginase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Schorderet D F
Department of Medicine, University of Washington, Seattle 98195.
Gartler S M
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.89.3.957
Published
1992-02-01
Pages
957-61
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC48364
Subset
IM
Grants
NICHD NIH HHS · HD-16659 · United States
External Links
PubMed source DOI: 10.1073/pnas.89.3.957 PMC Full Text View journal details
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