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

Abstract

DNA N-methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes, 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.

Deep6mA: a deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

“…A benchmark dataset is important to build a reliable prediction model. In this study, for convenience, we use the 6mA-rice-Lv dataset (17,18), including 154,000 positive samples and 154,000 negative samples, to evaluate the proposed method and to compare it with other methods. For each positive sample obtained from GEO, the sequence is 41nt long with the 6mA site locating at the center.…”

“…Koziol et al (2016) identified the 6mA modification in vertebrates by using HPLC, blots, and sequencing of methylated DNA Immunoprecipitation (MeDIP-seq). Zhou et al (2018) found through 6mA immunoprecipitation, mass spectrometry, and single molecule realtime that 0.2% of adenines in the rice genome are 6mA methylated and GAGG-rich sequences are the most significantly enriched for 6mA.…”

“…The above two prediction models were trained on 880 rice 6mA data and 880 non-6mA data and they did not consider the complex structure information in the sequence such as linkage disequilibrium between nucleotides, thus, there is still some room to improve. Zhou et al (2018) found 265,290 of rice 6mA data through a variety of experimental methods, such as HPLC-MS/MS, 6mA immunoprecipitation sequencing and Single Molecule Real-Time (SMRT), which enables us to train complex models for 6mA identification. For example, Lv et al (2019) provided a new random forest model named iDNA6mA-rice based on the reconstructed 154,000 6mA data and 154,000 non-6ma data.…”

FastFeatGen: Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites

“…We have obtained two balanced datasets, Dataset1 and Dataset2 from [33] and [31], respectively. Dataset1 contains 880 positive samples (6mA sites) and 880 negative samples (non-6mA sites).…”

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/ adenine methylation changes

“…Cytosine methylation is conventionally classified in terms of CG, CHG, and CHH sequence contexts (where H is A, C, or T), which are subjected to the actions of different DNA methyltransferases [9][10][11][12] . Methylation on adenine (N 6 -methyladenosine; 6mA) 7,13 has been recently found in Chlamydomonas and in several multicellular eukaryotes, including flowering plants 7,[14][15][16][17][18] . While in prokaryotes and ancient eukaryotes, 6mA serves as major marker to discriminate invasive foreign DNA 19 , its role in eukaryotes has recently been associated with transcriptional activation in response to stress 7,14 , and with transgenerational chromatin regulation 20 .…”