TY - JOUR
T1 - Methylation-specific digital karyotyping
AU - Hu, Min
AU - Yao, Jun
AU - Polyak, Kornelia
N1 - Funding Information:
ACKNOWLEDGMENTS The authors are supported by grants from the National Institutes of Health (CA89393, CA94074 and CA116235), Department of Defense (W8IXWH-04-1-0452), American Cancer Society (RSG-05-154-01-MGO) and the Susan G. Komen Foundation (PDF042234).
PY - 2006/8
Y1 - 2006/8
N2 - Epigenetic alterations, including DNA methylation and histone modifications, are known to regulate various physiological and pathological processes. In mammalian cells, DNA methylation occurs at cytosines of CpG dinucleotides. Several methods have been developed for the genome-wide analysis of methylation patterns. However, none of these are quantitative or sequence-based, and the identification of the exact location of the methylated CpG is difficult. In this protocol, we describe a recently developed method - methylation-specific digital karyotyping (MSDK) - that enables comprehensive and unbiased genome-wide DNA methylation analysis. Using a combination of a methylation-sensitive mapping enzyme (for example, AscI) and a fragmenting enzyme (for example, NlaIII), short sequence tags can be obtained and uniquely mapped to genome location. The number of tags in an MSDK library reflects the methylation status of the mapping enzyme sites. Generation of MSDK libraries can be completed in 7-10 days, whereas sequencing and data analysis requires an additional 3-4 weeks.
AB - Epigenetic alterations, including DNA methylation and histone modifications, are known to regulate various physiological and pathological processes. In mammalian cells, DNA methylation occurs at cytosines of CpG dinucleotides. Several methods have been developed for the genome-wide analysis of methylation patterns. However, none of these are quantitative or sequence-based, and the identification of the exact location of the methylated CpG is difficult. In this protocol, we describe a recently developed method - methylation-specific digital karyotyping (MSDK) - that enables comprehensive and unbiased genome-wide DNA methylation analysis. Using a combination of a methylation-sensitive mapping enzyme (for example, AscI) and a fragmenting enzyme (for example, NlaIII), short sequence tags can be obtained and uniquely mapped to genome location. The number of tags in an MSDK library reflects the methylation status of the mapping enzyme sites. Generation of MSDK libraries can be completed in 7-10 days, whereas sequencing and data analysis requires an additional 3-4 weeks.
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U2 - 10.1038/nprot.2006.278
DO - 10.1038/nprot.2006.278
M3 - Article
C2 - 17406428
AN - SCOPUS:34347217103
SN - 1754-2189
VL - 1
SP - 1621
EP - 1636
JO - Nature protocols
JF - Nature protocols
IS - 3
ER -