Comparative isoschizomer profiling of cytosine methylation: The HELP assay

Khulan, B., Thompson, R. F., Ye, K., Fazzari, M. J., Suzuki, M., Stasiek, E., Figueroa, M. E., Glass, J. L., Chen, Q., Montagna, C., Hatchwell, E., Selzer, R. R., Richmond, T. A., Green, R. D., Melnick, A., Greally, J. M. (2006) Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Research, 16 (8). pp. 1046-1055. ISSN 10889051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16809668
DOI: 10.1101/gr.5273806

Abstract

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. ©2006 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Subjects: organism description > animal > mammal > rodent > mouse
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein methylation
CSHL Authors:
Communities: CSHL labs
Depositing User: CSHL Librarian
Date: 2006
Date Deposited: 13 Dec 2011 15:13
Last Modified: 01 Mar 2013 15:51
PMCID: PMC1524864
Related URLs:
URI: https://repository.cshl.edu/id/eprint/22837

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