DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm

Deep learning based method for predicting DNA N6-methyladenosine sites

DNA N6 methyladenine (6mA) plays an important role in many biological processes, and accurately identifying its sites helps one to understand its biological effects more comprehensively. Previous traditional experimental methods are very labor-intensive and traditional machine learning methods also seem to be somewhat insufficient as the database of 6mA methylation groups becomes progressively larger, so we propose a deep learning-based method called multi-scale convolutional model based on global response normalization (CG6mA) to solve the prediction problem of 6mA site. This method is tested with other methods on three different kinds of benchmark datasets, and the results show that our model can get more excellent prediction results.

Misregulation of mitochondrial 6mA promotes the propagation of mutant mtDNA and causes aging in C. elegans

In virtually all eukaryotes, the mitochondrial DNA (mtDNA) encodes proteins necessary for oxidative phosphorylation (OXPHOS) and RNAs required for their synthesis. The mechanisms of regulation of mtDNA copy number and expression are not completely understood but crucially ensure the correct stoichiometric assembly of OXPHOS complexes from nuclear- and mtDNA-encoded subunits. Here, we detect adenosine N6-methylation (6mA) on the mtDNA of diverse animal and plant species. This modification is regulated in C. elegans by the DNA methyltransferase DAMT-1 and demethylase ALKB-1. Misregulation of mtDNA 6mA through targeted modulation of these activities inappropriately alters mtDNA copy number and transcript levels, impairing OXPHOS function, elevating oxidative stress, and shortening lifespan. Compounding these defects, mtDNA 6mA hypomethylation promotes the cross-generational propagation of a deleterious mtDNA. Together, these results reveal that mtDNA 6mA is highly conserved among eukaryotes and regulates lifespan by influencing mtDNA copy number, expression, and heritable mutation levels in vivo.

6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication

N6-methyladenine (6mA) DNA methylation has emerged as an important epigenetic modification in eukaryotes. Nevertheless, the evolution of the 6mA methylation of homologous genes after species and after gene duplications remains unclear in plants. To understand the evolution of 6mA methylation, we detected the genome-wide 6mA methylation patterns of four lotus plants (Nelumbo nucifera) from different geographic origins by nanopore sequencing and compared them to patterns in Arabidopsis and rice. Within lotus, the genomic distributions of 6mA sites are different from the widely studied 5mC methylation sites. Consistently, in lotus, Arabidopsis and rice, 6mA sites are enriched around transcriptional start sites, positively correlated with gene expression levels, and preferentially retained in highly and broadly expressed orthologs with longer gene lengths and more exons. Among different duplicate genes, 6mA methylation is significantly more enriched and conserved in whole-genome duplicates than in local duplicates. Overall, our study reveals the convergent patterns of 6mA methylation evolution based on both lineage and duplicate gene divergence, which underpin their potential role in gene regulatory evolution in plants.

A review of methods for predicting DNA N6-methyladenine sites

Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.

Plant synthetic epigenomic engineering for crop improvement

Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.

Distribution Pattern of N6-Methyladenine DNA Modification in the Seashore Paspalum (Paspalum vaginatum) Genome

N6-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, in some of them, it plays important role in the regulation process of stress-resistance response. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in halophyte Seashore paspalum (Paspalum vaginatum) remain largely unknown. Here, we examined the 6mA landscape in the P. vaginatum genome by adopting single molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the P. vaginatum genome. We demonstrated distinct 6mA methylation levels and 6mA distribution patterns in different types of transcription genes, which hinted at different epigenetic rules. Furthermore, the moderate 6mA density genes in P. vaginatum functionally correlated with stress resistance, which also maintained a higher transcriptional level. On the other hand, a specific 6mA distribution pattern in the gene body and near TSS was observed in gene groups with higher RNA expression, which maybe implied some kind of regularity between 6mA site distribution and the protein coding genes transcription was possible. Our study provides new insights into the association between 6mA methylation and gene expression, which may also contribute to key agronomic traits in P. vaginatum.

Same modification, different location: the mythical role of N6-adenine methylation in plant genomes

The present review summarizes recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics, discusses its importance in plant genomes, and highlights its chemical nature and functions. Adenine methylation is an epigenetic modification present in DNA (6mA) and RNA (m6A) that has a regulatory function in many cellular processes. This modification occurs through a reversible reaction that covalently binds a methyl group, usually at the N⁶ position of the purine ring. This modification carries biophysical properties that affect the stability of nucleic acids as well as their binding affinity with other molecules. DNA 6mA has been related to genome stability, gene expression, DNA replication, and repair mechanisms. Recent advances have shown that 6mA in plant genomes is related to development and stress response. In this review, we present recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics. We discuss the key elements of this modification, focusing mainly on its importance in plant genomes. Furthermore, we highlight its chemical nature and the regulatory effects that it exerts on gene expression and plant development. Finally, we emphasize the functions of 6mA in photosynthesis, stress, and flowering.

Rough fuzzy model based feature discretization in intelligent data preprocess

Feature discretization is an important preprocessing technology for massive data in industrial control. It improves the efficiency of edge-cloud computing by transforming continuous features into discrete ones, so as to meet the requirements of high-quality cloud services. Compared with other discretization methods, the discretization based on rough set has achieved good results in many applications because it can make full use of the known knowledge base without any prior information. However, the equivalence class of rough set is an ordinary set, which is difficult to describe the fuzzy components in the data, and the accuracy is low in some complex data types in big data environment. Therefore, we propose a rough fuzzy model based discretization algorithm (RFMD). Firstly, we use fuzzy c-means clustering to get the membership of each sample to each category. Then, we fuzzify the equivalence class of rough set by the obtained membership, and establish the fitness function of genetic algorithm based on rough fuzzy model to select the optimal discrete breakpoints on the continuous features. Finally, we compare the proposed method with the discretization algorithm based on rough set, the discretization algorithm based on information entropy, and the discretization algorithm based on chi-square test on remote sensing datasets. The experimental results verify the effectiveness of our method.

Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops

Epigenetic modifications alter the gene activity and function by causing change in the chromosomal architecture through DNA methylation/demethylation, or histone modifications without causing any change in DNA sequence. In plants, DNA cytosine methylation (5mC) is vital for various pathways such as, gene regulation, transposon suppression, DNA repair, replication, transcription, and recombination. Thanks to recent advances in high throughput sequencing (HTS) technologies for epigenomic “Big Data” generation, accumulated studies have revealed the occurrence of another novel DNA methylation mark, N6-methyladenosine (6mA), which is highly present on gene bodies mainly activates gene expression in model plants such as eudicot Arabidopsis (Arabidopsis thaliana) and monocot rice (Oryza sativa). However, in non-model crops, the occurrence and importance of 6mA remains largely less known, with only limited reports in few species, such as Rosaceae (wild strawberry), and soybean (Glycine max). Given the aforementioned vital roles of 6mA in plants, hereinafter, we summarize the latest advances of DNA 6mA modification, and investigate the historical, known and vital functions of 6mA in plants. We also consider advanced artificial-intelligence biotechnologies that improve extraction and prediction of 6mA concepts. In this Review, we discuss the potential challenges that may hinder exploitation of 6mA, and give future goals of 6mA from model plants to non-model crops.

A Mutation-Based Method for Pinpointing a DNA N6 -Methyladenine Methyltransferase Modification Site at Single Base Resolution

DNA N⁶ -methyladenine (6mA) has recently received notable attention due to an increased finding of its functional roles in higher eukaryotes. Here we report an enzyme-assisted chemical labeling method to pinpoint the DNA 6mA methyltransferase (MTase) substrate modification site at single base resolution. A designed allyl-substituted MTase cofactor was applied in the catalytic transfer reaction, and the allyl group was installed to the N⁶ -position of adenine within a specific DNA sequence to form N⁶ -allyladenine (6aA). The iodination of 6aA allyl group induced the formation of 1, N⁶ -cyclized adenine which caused mutations during DNA replication by a polymerase. Thus the modification site could be precisely detected by a mutation signal. We synthesized 6aA deoxynucleoside and deoxynucleotide model compounds and a 6aA-containing DNA probe, and screened nine DNA polymerases to define an optimal system capable of detecting the substrate modification site of a DNA 6mA MTase at single-base resolution.

New Insights into Plant Extracellular DNA. A Study in Soybean Root Extracellular Trap

exDNA is found in various organisms, including plants. However, plant exDNA has thus far received little attention related to its origin and role in the RET (root extracellular trap). In this study, we performed the first high-throughput genomic sequencing of plant exDNA from a Fabaceae with worldwide interest: soybean (Glycine max (L.) Merr.). The origin of this exDNA was first investigated in control condition, and the results show high-coverage on organelles (mitochondria/plastid) DNA relative to nuclear DNA, as well as a mix of coding and non-coding sequences. In the second part of this study, we investigated if exDNA release was modified during an elicitation with PEP-13 (a peptide elicitor from oomycete genus Phytophthora). Our results show that treatment of roots with PEP-13 does not affect the composition of exDNA.

DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage?

6-methyladenine (6mA) is fairly abundant in nuclear DNA of basal fungi, ciliates and green algae. In these organisms, 6mA is maintained near transcription start sites in ApT context by a parental-strand instruction dependent maintenance methyltransferase and is positively associated with transcription. In animals and plants, 6mA levels are high only in organellar DNA. The 6mA levels in nuclear DNA are very low. They are attributable to nucleotide salvage and the activity of otherwise mitochondrial METTL4, and may be considered as a price that cells pay for adenine methylation in RNA and/or organellar DNA. Cells minimize this price by sanitizing dNTP pools to limit 6mA incorporation, and by converting 6mA that has been incorporated into DNA back to adenine. Hence, 6mA in nuclear DNA should be described as an epigenetic mark only in basal fungi, ciliates and green algae, but not in animals and plants.