Tuesday, September 27, 2011

about methylation (甲基化)

'Methylation' has been more and more widely used in the field of gene regulation. Here is what I cracked:

  1. Methylation means addition of a methy- group to a subtract (see the right figure).
  2. Methylation can mean DNA methylation or protein methylation. 
  3. DNA methylation occurs in a CpG (C followed by G) site in DNA sequences, where cytosine (C) becomes 5-methylcytosine (see right figure, counting counterclockwise from the NH).
  4. About 80-90% of CpG sites in human DNA are methylated.
  5. Most CpG islands (i.e. CG% >65%) are un-methylated.
  6. Around 56% of mammalian genes has (un-methylated) CpG island in their promoter, like most housekeeping genes.
  7. In normal tissue, methylation of a gene is mainly localized to the coding region, which is CpG-poor. In contrast, the promoter region of the gene is unmethylated, despite a high density of CpG islands in the region.
  8. Methyl-seq is a technique combining DNA digestion by a methyl-sensitive enzyme HpaII and its methyl-insensitive isoschizomer MspI with the Illumina DNA sequencing platform.  Sequence tags present in MspI libraries but not in HpaII libraries are derived from methylated regions. Conversely, sequence tags that occur in HpaII libraries come from at least partially unmethylated regions.
  9. HpaII only digests 5'-CCGG-3' sites when the cytosine in the central CG dinucleotide is unmethylated, so the HpaII representation is enriched for the hypomethylated fraction of the genome. The MspI representation is a control for copy number changes and PCR amplification difficulties. Refer to HELP assay wiki page.
  10. Reduced Representation Bisulfite Sequencing (RRBS) is another method for DNA methylation. It has base-pair resolution. More detail can be refer her: http://genome-test.cse.ucsc.edu/cgi-bin/hgc?hgsid=3051149&o=181430182&t=181430183&g=wgEncodeHaibMethylRrbsK562HaibSitesRep1&i=K562_Rep3_RRBS

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