CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure

被引:13
作者
Cocozza, Sergio [1 ,2 ]
Akhtar, Most. Mauluda [1 ,2 ]
Miele, Gennaro [1 ,3 ,4 ]
Monticelli, Antonella [5 ]
机构
[1] Univ Napoli Federico II Univ Salerno, Grp Interdipartimentale Bioinformat & Biol Comput, Naples, Italy
[2] Univ Naples Federico 2, Dipartimento Biol & Patol Cellulare & Mol L Calif, Naples, Italy
[3] Univ Naples Federico 2, Dipartimento Sci Fis, Naples, Italy
[4] Ist Nazl Fis Nucl, Sez Napoli, I-80125 Naples, Italy
[5] CNR, Ist Endocrinol & Oncol Sperimentale, I-80125 Naples, Italy
关键词
DNA METHYLATION PATTERNS; CELLS; EPIGENETICS; SEQUENCE; EXPRESSION; ANIMALS; CULTURE;
D O I
10.1371/journal.pone.0023156
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];
摘要
DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more "protected" from methylation when compared with other regions of the genome.
引用
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页数:9
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