Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review

23 Scopus Citations
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Author(s)

  • Guan-Zheng Luo
  • Fang Wang
  • Xiaocheng Weng
  • Kai Chen
  • Ziyang Hao
  • Miao Yu
  • Jianzhao Liu
  • Chuan He

Detail(s)

Original languageEnglish
Article number11301
Journal / PublicationNature Communications
Volume7
Early online date15 Apr 2016
Publication statusE-pub ahead of print - 15 Apr 2016
Externally publishedYes

Abstract

Although extensively studied in prokaryotes, the prevalence and significance of DNA N6-methyladenine (6mA or m6dA) in eukaryotes had been underappreciated until recent studies, which have demonstrated that 6mA regulates gene expression as a potential heritable mark. To interrogate 6mA sites at single-base resolution, we report DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an approach that uses DpnI to cleave methylated adenine sites in duplex DNA. We find that DpnI cuts other sequence motifs besides the canonical GATC restriction sites, thereby expanding the utility of this method. DA-6mA-seq achieves higher sensitivity with nanograms of input DNA and lower sequencing depth than conventional approaches. We study 6mA at base resolution in the Chlamydomonas genome and apply the new method to two other eukaryotic organisms, Plasmodium and Penicillium. Combined with conventional approaches, our method further shows that most 6mA sites are fully methylated on both strands of DNA at various sequence contexts.

Citation Format(s)

Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. / Luo, Guan-Zheng; Wang, Fang; Weng, Xiaocheng; Chen, Kai; Hao, Ziyang; Yu, Miao; Deng, Xin; Liu, Jianzhao; He, Chuan.

In: Nature Communications, Vol. 7, 11301, 15.04.2016.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review