期刊
NUCLEIC ACIDS RESEARCH
卷 37, 期 12, 页码 3829-3839出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkp260
关键词
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资金
- Einstein Center for Epigenomics
- Bioinformatics Shared Resource and the Genomics Core Facility
- The National Institutes of Health (NIH) [R01 HG004401]
- NHLBI [R01 HL082946]
- NIA [P01 AG027734, R01 AG18728]
- NIGMS [T32 GM007288]
- Japan Society for the Promotion of Science
- Leukemia and Lymphoma Society Translational Research Award
- Hershaft Foundation
- Leukemia and Lymphoma Society
- NHGRI [R01 HG004401]
Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of < 200bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.
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