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First published online 10 October 2007
doi: 10.1242/dev.001131

Development 134, 3959-3965 (2007)
Published by The Company of Biologists 2007
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Genome-wide analysis of DNA methylation patterns

Daniel Zilberman1 and Steven Henikoff2,3

1 University of California, 211 Koshland Hall, Berkeley, CA 94720, USA.
2 Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
3 Howard Hughes Medical Institute, 1100 Fairview Avenue North, Seattle, WA 98109, USA.


Figure 1
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  		Fig. 1. Bisulfite conversion. DNA is denatured and then treated with sodium bisulfite to convert unmethylated cytosine to uracil, which is converted to thymine by PCR. An important point is that following bisulfite conversion, the DNA strands are no longer complementary, and primers are designed to assay the methylation (m) status of a specific strand.

 

Figure 2
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  		Fig. 2. Detecting DNA methylation with methylation-sensitive restriction enzymes. (A) A methylated (m) region of genomic DNA digested with HpaII (left) or MspI (right). Smaller fragments are discarded (red X), enriching for methylated DNA in the HpaII-treated sample, relative to the MspI-treated. (B) Genomic DNA is treated with McrBC, which cuts methylated (CH3) DNA. Smaller fragments are discarded, enriching for unmethylated DNA. There are many variations on these techniques (see Khulan et al., 2006Go; Lippman et al., 2004Go; Schumacher et al., 2006Go; Tompa et al., 2002Go).

 

Figure 3
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  		Fig. 3. Affinity enrichment of methylated DNA. Genomic DNA is denatured and then affinity purified with either an antibody (green) or a methyl-binding domain (MBD, red) protein that can be attached to a column (Cross et al., 1994Go; Weber et al., 2005Go).

 

Figure 4
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  		Fig. 4. Genomic analysis of DNA methylation. The suitability of a given technique of DNA methylation analysis depends on the genome size of the organism and the intended application. Bisulfite conversion coupled to Illumina bead arrays is well suited to the measurement of methylation polymorphism between multiple samples. A comprehensive analysis of methylation in organisms with small genomes can be accomplished with any one of a variety of techniques, whereas enrichment of unmethylated DNA is the preferred method when analyzing most vertebrate genomes.

 

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© The Company of Biologists Ltd 2007