Identification and analysis of adenine N 6-methylation sites in the rice genome

Chao Zhou, Changshi Wang, Hongbo Liu, Qiangwei Zhou, Qian Liu, Yan Guo, Ting Peng, Jiaming Song, Jianwei Zhang, Lingling Chen, Yu Zhao, Zhixiong Zeng, Dao Xiu Zhou

Research output: Contribution to journalLetter

44 Scopus citations

Abstract

DNA N6-methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes1–8, but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry, immunoprecipitation and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines are 6mA methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements. In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylcytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in transposable elements. We show that OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforce a distinct role for 6mA as a gene expression-associated epigenomic mark in eukaryotes.

Original languageEnglish (US)
Pages (from-to)554-563
Number of pages10
JournalNature plants
Volume4
Issue number8
DOIs
StatePublished - Aug 1 2018

ASJC Scopus subject areas

  • Plant Science

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    Zhou, C., Wang, C., Liu, H., Zhou, Q., Liu, Q., Guo, Y., Peng, T., Song, J., Zhang, J., Chen, L., Zhao, Y., Zeng, Z., & Zhou, D. X. (2018). Identification and analysis of adenine N 6-methylation sites in the rice genome. Nature plants, 4(8), 554-563. https://doi.org/10.1038/s41477-018-0214-x