DNA methylation and CpG islands

1. What is DNA methylation?
DNA methylation is one mechanism of epigenetic. Catalyzed by DNA methyltransferase (DNMT) enzyme, one methyl group has been added to the cytosine which convert the cytosine to methylcytosine. It usually happens at the carbon 5 position. Usually, the methylcytosine will spontaneous process the deamination and become thymine.
2. What is CpG sites?
 CpG sites represent for "-cytosine-phosphate-guanine" in a linear sequence. It should be distinguished from CG as base pair.
3. What is CpG islands?
CpG islands are DNA regions with high frequency of CpG sites. Usually, methylation is rare in CpG islands. It has been largely investigated because its closely related to transcriptional activity.
4. Function of DNA methylation.
DNA methylation has suggested being able to adjust gene expression since 1980s. DNA methylation could repress the gene expression by locking the gene. However, with further understanding of its function, more biological effect has been related to DNA methylation. For example, X chromosome inactivation, genomic imprinting, preservation of chromosome stability, and embryonic development.
With the application of next generation sequencing (NGS) technologies, investigation of DNA methylation is no longer restricted to the CpG island, especially CpG island located in the gene promoter. Genome-wide DNA methylation profile become available for us. It is worth noting that not only hypermethylation but also hypomethylation has been proved to be related to diseases, especially cancer. In fact, DNA methylation and cancer is a big topic which attract large attentions.

Many review has been published on this topic:


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19.          Wilhelm-Benartzi CS, Koestler DC, Karagas MR, et al. Review of processing and analysis methods for DNA methylation array data. British journal of cancer. Sep 17 2013;109(6):1394-1402.

20.          Laird PW. Principles and challenges of genome-wide DNA methylation analysis. Nature Reviews Genetics. 2010;11(3):191-203.

21.          Bock C. Analysing and interpreting DNA methylation data. Nature reviews. Genetics. Oct 2012;13(10):705-719.

22.          Ehrlich M. DNA hypomethylation in cancer cells. Epigenomics. Dec 2009;1(2):239-259.

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24.          Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nature genetics. Sep 26 2013;45(10):1127-1133.

25.          Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene. Aug 12 2002;21(35):5400-5413.

26.          Xu Z, Taylor JA. Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis. Feb 2014;35(2):356-364.

27.          Horvath S. DNA methylation age of human tissues and cell types. Genome biology. 2013;14(10):R115.

28.          Zykovich A, Hubbard A, Flynn JM, et al. Genome-wide DNA methylation changes with age in disease-free human skeletal muscle. Aging cell. Apr 2014;13(2):360-366.

29.          Duncan CG, Barwick BG, Jin G, et al. A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome research. Dec 2012;22(12):2339-2355.

30.          Huse JT, Aldape KD. The evolving role of molecular markers in the diagnosis and management of diffuse glioma. Clinical cancer research : an official journal of the American Association for Cancer Research. Nov 15 2014;20(22):5601-5611.