biostudies-literatureUnknown7(4)Cai WOrganisms and cells, in response to environmental influences or during development, undergo considerable changes in DNA methylation on a genome-wide scale, which are linked to a variety of biological processes. Using MethylC-seq to decipher DNA methylome at single-base resolution is prohibitively costly. In this study, we develop a novel approach, named MBRidge, to detect the methylation levels of repertoire CpGs, by innovatively introducing C-hydroxylmethylated adapters and bisulfate treatment into the MeDIP-seq protocol and employing ridge regression in data analysis. A systematic evaluation of DNA methylome in a human ovarian cell line T29 showed that MBRidge achieved high correlation (R > 0.90) with much less cost (∼10%) in comparison with MethylC-seq. We further applied MBRidge to proJournal of molecular cell biology299-313https://www.ebi.ac.uk/biostudies/studies/S-EPMC4542811biostudies-literatureMBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution.PMC4542811Wu JCai TSun ZSZhao FMao FTeng HCai WfalseMBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution.Organisms and cells, in response to environmental influences or during development, undergo considerable changes in DNA methylation on a genome-wide scale, which are linked to a variety of biological processes. Using MethylC-seq to decipher DNA methylome at single-base resolution is prohibitively costly. In this study, we develop a novel approach, named MBRidge, to detect the methylation levels of repertoire CpGs, by innovatively introducing C-hydroxylmethylated adapters and bisulfate treatment into the MeDIP-seq protocol and employing ridge regression in data analysis. A systematic evaluation of DNA methylome in a human ovarian cell line T29 showed that MBRidge achieved high correlation (R > 0.90) with much less cost (∼10%) in comparison with MethylC-seq. We further applied MBRidge to pro2015-01-01T00:00:00Z2015 Aug2025-04-19T08:29:38.666Z2019-03-27T01:57:04ZS-EPMC45428112607836210.1093/jmcb/mjv037