Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Issue 10 (3rd October 2022)

• Record Type: Journal Article
• Authors: Han, Yanan; Zheleznyakova, Galina Yurevna; Marincevic-Zuniga, Yanara; Kakhki, Majid Pahlevan; Raine, Amanda; Needhamsen, Maria; Jagodic, Maja
• Is Part Of: Epigenetics. Volume 17:Issue 10(2022)
• Page Start: 1195
• Page End: 1204
• Publication Date: 2022-10-03
• Subjects: Low input DNA -- methylome -- EM-seq -- PBAT; Epigenesis -- Periodicals; Epigenetica; 572.86505
• DOI: 10.1080/15592294.2021.1997406
• Languages: English
• ISSNs: 1559-2294

Abstract

ABSTRACT: 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.