MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae

Liu, Zhaoyu; Xing, Jian-Feng; Chen, Wei; Luan, Meiwei; Xie, Rui; Huang, Jing; Xie, Shuang; Xiao, Chuan-Le

doi:10.1038/s41438-019-0160-4

Cited by 56 publications

(35 citation statements)

References 39 publications

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“…DNA 6mA modification had been characterized in several eukaryotes in recent studies and was involved in regulating gene expression (Liang et al, 2018;Xiao et al, 2018;Liu et al, 2019;Luan et al, 2019). The aberrational transcription of noncoding gene, as an important epigenetic control element, could also exert a great impact on important biological processes (Ling et al, 2013;Luo et al, 2017;Gomez-Orte et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes

et al. 2020

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N6-methyladenosine (6mA) DNA modification played an important role in epigenetic regulation of gene expression. And the aberrational expression of non-coding genes, as important regular elements of gene expression, was related to many diseases. However, the distribution and potential functions of 6mA modification in non-coding RNA (ncRNA) genes are still unknown. In this study, we analyzed the 6mA distribution of ncRNA genes and compared them with protein-coding genes in four species (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens) using singlemolecule real-time (SMRT) sequencing data. The results indicated that the consensus motifs of short nucleotides at 6mA location were highly conserved in four species, and the non-coding gene was less likely to be methylated compared with proteincoding gene. Especially, the 6mA-methylated lncRNA genes were expressed significant lower than genes without methylation in A. thaliana (p = 3.295e-4), D. melanogaster (p = 3.439e-11), and H. sapiens (p = 9.087e-3). The detection and distribution profiling of 6mA modification in ncRNA regions from four species reveal that 6mA modifications may have effects on their expression level.

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Section: Discussionmentioning

confidence: 99%

Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes

et al. 2020

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“…Following procedures similar to our benchmark dataset construction, we have constructed two independent test datasets in order to evaluate the robustness of our proposed tool in terms of N 6 -Methyladenine site identification in plant genome. Fragaria Vesca (Wild strawberry) and Arabidopsis thaliana (cress weed plant) 6mA site containing sequences have been obtained from the MDR database [39] and from NCBI GEO with accession number GSE81597 [40], respectively. Performance of i6mA-CNN on these datasets have been shown in detail in Table 4.…”

Section: Resultsmentioning

confidence: 99%

A Convolution Based Computational Approach Towards DNA N6-methyladenine Site Identification and Motif Extraction in Rice Genome

Rahman

Amin

Shatabda

et al. 2020

Preprint

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ABSTRACTDNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification and is responsible for many biological functions. Experimental methods for genome wide 6mA site detection is an expensive and manual labour intensive process. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network based tool i6mA-CNN capable of identifying 6mA sites in the rice genome. Our model coordinates among multiple types of features such as PseAAC inspired customized feature vector, multiple one hot representations and dinucleotide physicochemical properties. It achieves area under the receiver operating characteristic curve of 0.98 with an overall accuracy of 0.94 using 5 fold cross validation on benchmark dataset. Finally, we evaluate our model on two other plant genome 6mA site identification datasets besides rice. Results suggest that our proposed tool is able to generalize its ability of 6mA site identification on plant genomes irrespective of plant species. Supplementary data (benchmark dataset, independent test dataset, comparison purpose dataset, trained model, physicochemical property values, attention mechanism details for motif finding) are available at Nucleic Acids Research online. Web tool for this research can be found here.

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“…Until recently, the 6mA abundance and distribution has been investigated in a small number of plants [30,46,56,57], unicellular algae [58] and multilineage fungi [59]. The 6mA levels show considerable variation in prevalence and effect on gene expression in different species owing to their different distribution patterns.…”

Section: Abundance Of 6ma Level In Plants and Possible Functional Impmentioning

confidence: 99%

DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code

Karanthamalai

Chodon

Chauhan

et al. 2020

Plants

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N6-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due to its undetectable level. However, with the new advancements in methods, considerable 6mA distribution is identified across the plant genome. Unlike 5-methylcytosine (5mC) in the gene promoter, 6mA does not have a definitive role in repression but is exposed to have divergent regulation in gene expression. Though 6mA information is less known, the available evidences suggest its function in plant development, tissue differentiation, and regulations in gene expression. The current review article emphasizes the research advances in DNA 6mA modifications, identification, available databases, analysis tools and its significance in plant development, cellular functions and future perspectives of research.

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MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae

Cited by 56 publications

References 39 publications

Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes

Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes

A Convolution Based Computational Approach Towards DNA N6-methyladenine Site Identification and Motif Extraction in Rice Genome

DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code

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