期刊
GENOMICS
卷 107, 期 4, 页码 109-119出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2016.03.001
关键词
Restriction enzyme; CpG; DNA methylation; Next-generation sequencing
资金
- AFR PhD grant from the Fonds National de la Recherche (FNR) [1176135, C12/BM/3985792]
- Luxembourg Institute of Health (LIH)
- Ministry of Higher Education and Research of Luxembourg
Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. As the current best estimate suggests that only similar to 20% of CpGs are dynamically regulated, we characterised the CpG and genomic context surrounding all suitable restriction enzyme sites to identify those that were located in regions rich in dynamically methylated CpGs. The restriction-site distributions for MspI, BstUI, and HhaI were non-random. CpGs in CGI and shelf + shore could be enriched, particularly in gene bodies for all genomic regions, promoters (TSS1500, TSS200), intra- (1st exon, gene body, 3'UTR, 5'UTR) and inter-genic regions. HpyCH4IV enriched CpG elements in the open sea for all genomic elements. Judicious restriction enzyme choice improves the focus of reduced representation approaches by avoiding the monopolization of read coverage by genomic regions that are irrelevant, unwanted or difficult to map, and only sequencing the most informative fraction of CpGs. (C) 2016 Elsevier Inc. All rights reserved.
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