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Comment
. 2010 Apr;42(4):279.
doi: 10.1038/ng0410-279.

Genome-wide analysis of palindrome formation

Scott J Diede, Hisashi Tanaka, Donald A Bergstrom, Meng-Chao Yao, Stephen J Tapscott
Comment

Genome-wide analysis of palindrome formation

Scott J Diede et al. Nat Genet. 2010 Apr.
No abstract available

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Figures

Figure 1
Figure 1
Specific enrichment for either CpG methylation or DNA palindromes using the GAPF assay. Shown are results from Colo320DM cells of a PCR-based enrichment assay after one round of GAPF (GAPF ×1), two rounds of GAPF (GAPF ×2), or GAPF with 50% formamide added. The assay was performed in duplicate. PCR products obtained using unprocessed genomic DNA (gDNA) are included for comparison. As a negative control, the PCR product labeled as Tel amplifies a region on chromosome 1 that does not contain a DNA palindrome or CpG methylation, and primers to generate this fragment are added for multiplex PCR in each of the loci evaluated. A nonpalindromic GAPF-positive locus that is differentially CpG methylated (HAND2) is recalcitrant to a second round of GAPF. The DNA palindrome at the CTSK locus is enriched after one round of GAPF but does not survive the second round. This pattern is also recapitulated for a naturally occurring DNA palindrome on chromosome 6 (IR6-107.3). The addition of 50% formamide during denaturation optimizes GAPF for DNA palindromes, as shown by the enrichment for the CTSK and IR6-107.3 DNA palindromes, while abolishing the signal from the methylated HAND2 locus.
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