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

Hae Min Jeong; Sangseon Lee; Heejoon Chae; RyongNam 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

Epigenomics. 2016 Aug;8(8):1061-77. doi: 10.2217/epi-2016-0038. Epub 2016 Jun 8.

Authors

Hae Min Jeong¹, Sangseon Lee², Heejoon Chae³, RyongNam Kim^{1

4}, Mi Jeong Kwon^{5

6}, Ensel Oh^{7

8}, Yoon-La Choi^{7

8

9}, Sun Kim^{10

11

12}, Young Kee Shin^{1

4

12

13

14}

Affiliations

¹ Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
² School of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.
³ Computer Science Department, School of Informatics & Computing, Indiana University, Bloomington, IN, USA.
⁴ Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea.
⁵ College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
⁶ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
⁷ Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
⁸ Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.
⁹ Laboratory of Cancer Genomics & Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea.
¹⁰ Department of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.
¹¹ Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
¹² Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
¹³ The Center for Anti-Cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Republic of Korea.
¹⁴ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.

PMID: 27266718
DOI: 10.2217/epi-2016-0038

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.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

DNA Methylation*
Genome
High-Throughput Nucleotide Sequencing / methods*
High-Throughput Nucleotide Sequencing / standards
Humans
Liver Neoplasms / genetics*
Sequence Analysis, DNA / methods*
Sequence Analysis, DNA / standards
Stomach Neoplasms / genetics*