气候变化领域集成服务门户(CCPortal): Genome-wide detection of cytosine methylation by single molecule real-time sequencing

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DOI	10.1073/pnas.2019768118
	Genome-wide detection of cytosine methylation by single molecule real-time sequencing
	Tse O.Y.O.; Jiang P.; Cheng S.H.; Peng W.; Shang H.; Wong J.; Chan S.L.; Poon L.C.Y.; Leung T.Y.; Chan K.C.A.; Chiu R.W.K.; Lo Y.M.D.
发表日期	2021
ISSN	00278424
卷号	118 期号:5
英文摘要	5-Methylcytosine (5mC) is an important type of epigenetic modification. Bisulfite sequencing (BS-seq) has limitations, such as severe DNA degradation. Using single molecule real-time sequencing, we developed a methodology to directly examine 5mC. This approach holistically examined kinetic signals of a DNA polymerase (including interpulse duration and pulse width) and sequence context for every nucleotide within a measurement window, termed the holistic kinetic (HK) model. The measurement window of each analyzed double-stranded DNA molecule comprised 21 nucleotides with a cytosine in a CpG site in the center. We used amplified DNA (unmethylated) and M.SssI-treated DNA (methylated) (M.SssI being a CpG methyltransferase) to train a convolutional neural network. The area under the curve for differentiating methylation states using such samples was up to 0.97. The sensitivity and specificity for genome-wide 5mC detection at single-base resolution reached 90% and 94%, respectively. The HK model was then tested on human–mouse hybrid fragments in which each member of the hybrid had a different methylation status. The model was also tested on human genomic DNA molecules extracted from various biological samples, such as buffy coat, placental, and tumoral tissues. The overall methylation levels deduced by the HK model were well correlated with those by BS-seq (r = 0.99; P < 0.0001) and allowed the measurement of allele-specific methylation patterns in imprinted genes. Taken together, this methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses. © 2020 Proceedings of the National Academy of Sciences of the United States of America. All rights reserved.
英文关键词	Base modifications; Epigenetics; Epigenomics; Third-generation sequencing
语种	英语
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180791
作者单位	Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; Department of Chemical Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; Department of Clinical Oncology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; State Key Laboratory of Translational Oncology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; Department of Obstetrics and Gynaecology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
推荐引用方式 GB/T 7714	Tse O.Y.O.,Jiang P.,Cheng S.H.,et al. Genome-wide detection of cytosine methylation by single molecule real-time sequencing[J],2021,118(5).
APA	Tse O.Y.O..,Jiang P..,Cheng S.H..,Peng W..,Shang H..,...&Lo Y.M.D..(2021).Genome-wide detection of cytosine methylation by single molecule real-time sequencing.Proceedings of the National Academy of Sciences of the United States of America,118(5).
MLA	Tse O.Y.O.,et al."Genome-wide detection of cytosine methylation by single molecule real-time sequencing".Proceedings of the National Academy of Sciences of the United States of America 118.5(2021).