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

Guan-Zheng Luo, Fang Wang, Xiaocheng Weng, Kai Chen, Ziyang Hao, Miao Yu, Xin Deng, Jianzhao Liu and Chuan He ()
Additional contact information
Guan-Zheng Luo: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Fang Wang: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Xiaocheng Weng: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Kai Chen: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Ziyang Hao: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Miao Yu: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Xin Deng: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Jianzhao Liu: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago
Chuan He: Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago

Nature Communications, 2016, vol. 7, issue 1, 1-6

Abstract: 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.

Date: 2016
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms11301 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11301

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms11301

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().