Comparative isoschizomer profiling of cytosine methylation: The HELP assay

Batbayar Khulan, Reid F. Thompson, Kenny Ye, Melissa J. Fazzari, Masako Suzuki, Edyta Stasiek, Maria E. Figueroa, Jacob L. Glass, Quan Chen, Cristina Montagna, Eli Hatchwell, Rebecca R. Selzer, Todd A. Richmond, Roland D. Green, Ari Melnick, John M. Greally

Research output: Contribution to journalArticlepeer-review

341 Scopus citations


The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its methylation-insensitive isoschizomer. This assay, termed HELP (HpaII tiny fragment Enrichment by Ligation-mediated PCR), allows both intragenomic profiling and intergenomic comparisons of cytosine methylation. The intragenomic profile shows most of the genome to be contiguous methylated sequence with occasional clusters of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing confirmed the four candidates tested to be T-DMRs, while quantitative RT-PCR for two genes with T-DMRs located at their promoters showed the HELP data to be correlated with gene activity at these loci. The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome.

Original languageEnglish (US)
Pages (from-to)1046-1055
Number of pages10
JournalGenome Research
Issue number8
StatePublished - 2006
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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