期刊
EPIGENETICS
卷 17, 期 10, 页码 1195-1204出版社
TAYLOR & FRANCIS INC
DOI: 10.1080/15592294.2021.1997406
关键词
Low input DNA; methylome; EM-seq; PBAT
资金
- European Union's Horizon 2020 research, innovation programme [733161]
- European Research Council (ERC) [818170]
- Swedish Research Council (VR)
- Swedish Brain Foundation
- Swedish MS Foundation
- Stockholm County Council (ALF project)
- European Research Council (ERC) [818170] Funding Source: European Research Council (ERC)
This study compared two different DNA methylation quantification methods and found that enzymatic methyl-seq (EM-seq) performed better in terms of library and sequencing quality, especially in CpG coverage, CpG site overlap, and consistency between input series.
DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.
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