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DNA unmethylome profiling via covalent capture of CpG sites

ABSTRACT: Cytosine 5-modification is a widespread epigenetic mark in eukaryote genomes including humans, but its large scale populational studies are hampered by substantial limitations of the existing analytical techniques. We have developed a new approach for mapping of the unmodified fraction of the genome, i.e. DNA unmethylome, which is based on covalent tagging of unmodified CpG sites with biotin. Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the S-adenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group. Analysis of the streptavidin-enriched human unmethylome on tiling DNA microarrays showed that the new approach (named mTAG-chip) offers nanogram sensitivity, a substantially higher precision in the low and medium CpG density regions and added versatility as compared with the existing epigenome profiling techniques.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36305 | GEO | 2012/03/08

SECONDARY ACCESSION(S): PRJNA153051

REPOSITORIES: GEO

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DNA unmethylome profiling via covalent capture of CpG sites

Project description:Cytosine 5-modification is a widespread epigenetic mark in eukaryote genomes including humans, but its large scale populational studies are hampered by substantial limitations of the existing analytical techniques. We have developed a new approach for mapping of the unmodified fraction of the genome, i.e. DNA unmethylome, which is based on covalent tagging of unmodified CpG sites with biotin. Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the S-adenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group. Analysis of the streptavidin-enriched human unmethylome on tiling DNA microarrays showed that the new approach (named mTAG-chip) offers nanogram sensitivity, a substantially higher precision in the low and medium CpG density regions and added versatility as compared with the existing epigenome profiling techniques. AC103, AC13 and AC31 are DNA samples from three postmortem brains. Nr1 and Nr2 are two replicates of each sample. 5%, 20% and 70% are labeling efficiency. K means 0% labeling efficiency. We were testing which labeling efficiency was best by comparing to published seq data using correlation.

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