Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

BMC Genomics

Methodology Article

Lili Li¹  Qian Tao¹  Xiuqing Zhang²  Yudong Xia²  Na Yi²  Desheng Gong²  Fei Gao²  Junwen Wang²  Yu Yao²  Hanlin Lu²  Honglong Wu²  Huijuan Luo² 

[1] Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, SAR, China;Science & Technology Department, BGI-Shenzhen, No.11, Bei Shan Industrial Zone, Yantian DistrictShenzhen, China;

关键词: Single-enzyme RRBS;    Double-enzyme RRBS;    DNA methylation;    CpG coverage;   

DOI  :  10.1186/1471-2164-14-11

 received in 2012-08-17, accepted in 2013-01-11,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundReduced representation bisulfite sequencing (RRBS) was developed to measure DNA methylation of high-CG regions at single base-pair resolution, and has been widely used because of its minimal DNA requirements and cost efficacy; however, the CpG coverage of genomic regions is restricted and important regions with low-CG will be ignored in DNA methylation profiling. This method could be improved to generate a more comprehensive representation.ResultsBased on in silico simulation of enzyme digestion of human and mouse genomes, we have optimized the current single-enzyme RRBS by applying double enzyme digestion in the library construction to interrogate more representative regions. CpG coverage of genomic regions was considerably increased in both high-CG and low-CG regions using the double-enzyme RRBS method, leading to more accurate detection of their average methylation levels and identification of differential methylation regions between samples. We also applied this double-enzyme RRBS method to comprehensively analyze the CpG methylation profiles of two colorectal cancer cell lines.ConclusionThe double-enzyme RRBS increases the CpG coverage of genomic regions considerably over the previous single-enzyme RRBS method, leading to more accurate detection of their average methylation levels. It will facilitate genome-wide DNA methylation studies in multiple and complex clinical samples.

【 授权许可】

Unknown   
© Wang et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.