期刊
NATURE BIOTECHNOLOGY
卷 28, 期 10, 页码 1097-U194出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.1682
关键词
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资金
- National Institute on Drug Abuse (NIDA)
- NIH [5U01ES017154-02, 5U01DA025956-02, 6U01ES017155-02, 5U01ES017166-02, T32 CA108462-04, F32CA141799, T32 CA108462-06, T32 GM008568]
- CIRM [TB1-01190]
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant ( their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.
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