Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis

Hae Min Jeong; Sangseon Lee; Heejoon Chae; Ryong Nam Kim; Mi Jeong Kwon; Ensel Oh; Yoon La Choi; Sun Kim; Young Kee Shin

doi:10.2217/epi-2016-0038

Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis

Hae Min Jeong, Sangseon Lee, Heejoon Chae, Ryong Nam Kim, Mi Jeong Kwon, Ensel Oh, Yoon La Choi, Sun Kim, Young Kee Shin

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

Aims: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. Materials & methods: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. Results: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. Conclusion: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

Original language	English
Pages (from-to)	1061-1077
Number of pages	17
Journal	Epigenomics
Volume	8
Issue number	8
DOIs	https://doi.org/10.2217/epi-2016-0038
State	Published - Aug 2016

Keywords

DNA methylation analysis
methylated DNA immunoprecipitation-bisulphite sequencing
next-generation sequencing

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.2217/epi-2016-0038

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title = "Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis",

abstract = "Aims: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. Materials & methods: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. Results: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. Conclusion: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.",

keywords = "DNA methylation analysis, methylated DNA immunoprecipitation-bisulphite sequencing, next-generation sequencing",

author = "Jeong, {Hae Min} and Sangseon Lee and Heejoon Chae and Kim, {Ryong Nam} and Kwon, {Mi Jeong} and Ensel Oh and Choi, {Yoon La} and Sun Kim and Shin, {Young Kee}",

note = "Publisher Copyright: {\textcopyright} 2016 Shin et al.",

year = "2016",

month = aug,

doi = "10.2217/epi-2016-0038",

language = "English",

volume = "8",

pages = "1061--1077",

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T1 - Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis

AU - Jeong, Hae Min

AU - Lee, Sangseon

AU - Chae, Heejoon

AU - Kim, Ryong Nam

AU - Kwon, Mi Jeong

AU - Oh, Ensel

AU - Choi, Yoon La

AU - Kim, Sun

AU - Shin, Young Kee

PY - 2016/8

Y1 - 2016/8

N2 - Aims: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. Materials & methods: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. Results: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. Conclusion: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

AB - Aims: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. Materials & methods: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. Results: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. Conclusion: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

KW - DNA methylation analysis

KW - methylated DNA immunoprecipitation-bisulphite sequencing

KW - next-generation sequencing

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DO - 10.2217/epi-2016-0038

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SN - 1750-1911

VL - 8

SP - 1061

EP - 1077

JO - Epigenomics

JF - Epigenomics

IS - 8

ER -

Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis

Abstract

Keywords

UN SDGs

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