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Thursday, July 29, 2010

Mapping the Human Genome

I searched via Google Scholar to see if it is currently possible to map the human genome or that of any other mammal. The human genome was "mapped" in terms of four bases before the discovery of another two nucleotides, viz., 5-hydroxymethylcytosine and 5-methylcytosine, which are crucial to mammalian development. I found this paper:

Nucleic Acids Research Advance Access published online on April 5, 2010
Nucleic Acids Research, doi:10.1093/nar/gkq223
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© The Author(s) 2010. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


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Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
Seung-Gi Jin, Swati Kadam and Gerd P. Pfeifer*
Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA

*To whom correspondence should be addressed. Tel: +1 626 301 8853 begin_of_the_skype_highlighting +1 626 301 8853 end_of_the_skype_highlighting; Fax: +1 626 358 7703; Email:

Received November 5, 2009. Revised March 12, 2010. Accepted March 17, 2010.

DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression control and disease pathogenesis. Different technologies have been developed to examine the distribution of 5-methylcytosine (5mC) in specific sequences of the genome. Recently, substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic oxidation of 5mC by TET1, have been detected in certain mammalian tissues. Here, we have examined the ability of several commonly used DNA methylation profiling methods to distinguish between 5mC and 5hmC. We show that techniques based on sodium bisulfite treatment of DNA are incapable of distinguishing between the two modified bases. In contrast, techniques based on immunoprecipitation with anti-5mC antibody (methylated DNA immunoprecipitation, MeDIP) or those based on proteins that bind to methylated CpG sequences (e.g. methylated-CpG island recovery assay, MIRA) do not detect 5hmC and are specific for 5mC unless both modified bases occur in the same DNA fragment. We also report that several methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to sequences containing 5hmC. Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base.


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