RT Journal
A1 Khulan, Batbayar
A1 Thompson, Reid F.
A1 Ye, Kenny
A1 Fazzari, Melissa J.
A1 Suzuki, Masako
A1 Stasiek, Edyta
A1 Figueroa, Maria E.
A1 Glass, Jacob L.
A1 Chen, Quan
A1 Montagna, Cristina
A1 Hatchwell, Eli
A1 Selzer, Rebecca R.
A1 Richmond, Todd A.
A1 Green, Roland D.
A1 Melnick, Ari
A1 Greally, John M.
T1 Comparative isoschizomer profiling of cytosine methylation: The HELP assay
JF Genome Research 
JO Genome Research 
YR 2006 
FD August 01 
VO 16 
IS 8 
SP 1046 
OP 1055 
DO 10.1101/gr.5273806 
UL http://genome.cshlp.org/content/16/8/1046.abstract 
AB 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.