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Open Access Highly Accessed Methodology article

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

Xiaojun Huang12, Hanlin Lu1, Jun-Wen Wang1, Liqin Xu13, Siyang Liu1, Jihua Sun1 and Fei Gao1*

Author Affiliations

1 Science & Technology Department, BGI-Shenzhen, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China

2 College of Life Sciences, Wuhan University, Luojia Road No.16, Wuchang District, Wuhan 430072, China

3 School of Life Science and Technology, University of Electronic Science and Technology of China, No.4, Section 2, North Jianshe Road, Chengdu 610054, China

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BMC Genetics 2013, 14:56  doi:10.1186/1471-2156-14-56

Published: 18 June 2013

Abstract

Background

As a well-known epigenomic modification, DNA methylation is found to be common in plants and plays an important role in many biological processes. Relying on the unique feature of methylation-dependent digestion, the family of methylation-requiring restriction-like endonuclease, such as MspJI and its homologs, was suggested for a potential usage in methylation detection.

Results

In this study, we combine MspJI digestion and electrophoretic band selection with next generation high-throughput sequencing technology to detect 5-methylcytosines in Arabidopsis genome. By developing a bioinformatics workflow to attribute the CNNR sites recognized by MspJI to the reference genome, we fulfilled the systematic assessment of this method.

Conclusions

According to the assessment, here we provide the method for generating a detailed map of plant methylome that could be feasible, reliable and economical in methylation investigation.

Keywords:
MspJI; DNA methylation; Arabidopsis