TY - JOUR
T1 - CpG distribution patterns in methylated and non-methylated species
AU - Shimizu, Tom S.
AU - Takahashi, Kouichi
AU - Tomita, Masaru
N1 - Funding Information:
The authors would like to thank Drs Edward Trifonov, Akihiro Umezawa and Masahiko Mizuno for helpful comments and Kenta Hashimoto for programming in the early stage of this research. This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas 'Genome Science' from the Ministry of Education and Science in Japan.
PY - 1997/12/31
Y1 - 1997/12/31
N2 - To characterize the extent of DNA methylation and its possible biological roles in a wide variety of organisms, we have analyzed gene sequences extracted from the GenBank database. Sequences of both methylated and non-methylated species were used for comparative analysis. The local CpG dinucleotide distribution near the 5' ends of genes as well as the degree of overall CpG suppression/depletion in the entire gene region were examined in all complete gene sequences for each species. We show that the distribution patterns of CpG near the 5' region of genes differ among vertebrates, invertebrates, plants and bacteria. CpG island-like peaks in CpG O/E (observed/expected ratio) were observed not only in methylated species, but also in non-methylated species. In methylated non-vertebrates, overall CpG O/E values were lower, and peaks in the CpG profile of 5' regions were larger than in non-methylated species. We discuss the implications of such biases with respect to DNA methylation.
AB - To characterize the extent of DNA methylation and its possible biological roles in a wide variety of organisms, we have analyzed gene sequences extracted from the GenBank database. Sequences of both methylated and non-methylated species were used for comparative analysis. The local CpG dinucleotide distribution near the 5' ends of genes as well as the degree of overall CpG suppression/depletion in the entire gene region were examined in all complete gene sequences for each species. We show that the distribution patterns of CpG near the 5' region of genes differ among vertebrates, invertebrates, plants and bacteria. CpG island-like peaks in CpG O/E (observed/expected ratio) were observed not only in methylated species, but also in non-methylated species. In methylated non-vertebrates, overall CpG O/E values were lower, and peaks in the CpG profile of 5' regions were larger than in non-methylated species. We discuss the implications of such biases with respect to DNA methylation.
KW - CpG distribution patterns
KW - DNA methylation
KW - Methylated species
KW - Non-methylated species
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U2 - 10.1016/S0378-1119(97)00542-8
DO - 10.1016/S0378-1119(97)00542-8
M3 - Article
C2 - 9461383
AN - SCOPUS:0031593246
SN - 0378-1119
VL - 205
SP - 103
EP - 107
JO - Gene
JF - Gene
IS - 1-2
ER -