Identification and analysis of adenine N6-methylation sites in the rice genome

We report the application of 6mA IP-sequencing technology for high-throughput profiling in rice tissues of 12 days' leaf. By obtaining over 20 million high quality clean mapping sequenced reads from immunoprecipitated DNA, we generate genome-wide 6mA maps of rice 12 days' leaf. Using mass spectrometry and 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 (TEs). In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylated cytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in TEs. 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 reinforces a distinct role for 6mA as a gene-expression associated epigenomic mark in eukaryotes. Examination of 6mA modification in 12 days' leaves； The raw data of rice genome PacBio sequencing is available under SRA accession number SRP071598. And the download link is https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP071598 .