DNA N6-adenine methylation in Arabidopsis thaliana

Liang, Zhe; Shen, Lisha; Cui, Xuean; Bao, Shengjie; Geng, Yuke; Yu, Guoliang; Liang, Fan; Lu, Tiegang; Gu, Xiaofeng; Yu, Hao

doi:10.1016/j.mod.2017.04.384

Cited by 20 publications

(31 citation statements)

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“…Local DNA methylation variants can have major effects on the transcription of neighbouring genes and can be inherited over generations (Diez et al, 2014). DNA methylation of 6mA has been found to be a potentially epigenetic marker in several eukaryotes (Liang et al, 2018;Zhou et al, 2018). Nevertheless, the specific distribution of motifs and potential effects of such modifications in plant genomes, remain poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

et al. 2020

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Section: Introductionmentioning

confidence: 99%

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

et al. 2020

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“…In this study, we generated PacBio RSII reads using unamplified gDNA to investigate the genome‐wide DNA modification landscape, using landmarks such as 6mA (Greer et al ., ; Zhang et al ., ; Liang et al ., ) and 4mC (Iyer et al ., ). In total, we found 6956 and 9517 sites for 6mA and 4mC, respectively (Table S9).…”

Section: Resultsmentioning

confidence: 99%

“…Here, we presented a genome‐wide landscape of DNA modification and identified 6956 and 9517 sites for 6mA and 4mC, respectively. In Arabidopsis, there are 29 811 adenines including 6mA in total (Liang et al ., ). Given the relatively low coverage of PacBio data of C. equis .…”

Section: Discussionmentioning

confidence: 97%

“…DNA modifications, such as 6mA, were discovered in Chlamydomonas (Fu et al ., ), Escherichia coli (Fang et al ., ), Arabidopsis (Liang et al ., ), C. elegans (Greer et al ., ) and Drosophila (Zhang et al ., ). Previous studies showed that PacBio SMRT sequencing works well to detect DNA modifications (Fang et al ., ; Liang et al ., ; Zhu et al ., ). So the assembly genome and PacBio long reads in this study provided unprecedented insights into the DNA modifications in C. equis .…”

Section: Discussionmentioning

confidence: 99%

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De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

Ye¹,

Zhang

Chen³

et al. 2019

The Plant Journal

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These authors contributed equally to this work. SUMMARYCasuarina equisetifolia (C. equisetifolia), a conifer-like angiosperm with resistance to typhoon and stress tolerance, is mainly cultivated in the coastal areas of Australasia. C. equisetifolia, making it a valuable model to study secondary growth associated genes and stress-tolerance traits. However, the genome sequence is unavailable and therefore wood-associated growth rate and stress resistance at the molecular level is largely unexplored. We therefore constructed a high-quality draft genome sequence of C. equisetifolia by a combination of Illumina second-generation sequencing reads and Pacific Biosciences single-molecule real-time (SMRT) long reads to advance the investigation of this species. Here, we report the genome assembly, which contains approximately 300 megabases (Mb) and scaffold size of N50 is 1.06 Mb. Additionally, gene annotation, assisted by a combination of prediction and RNA-seq data, generated 29 827 annotated protein-coding genes and 1983 non-coding genes, respectively. Furthermore, we found that the total number of repetitive sequences account for one-third of the genome assembly. Here we also construct the genome-wide map of DNA modification, such as two novel forms N 6 -adenine (6mA) and N4-methylcytosine (4mC) at the level of single-nucleotide resolution using single-molecule real-time (SMRT) sequencing. Interestingly, we found that 17% of 6mA modification genes and 15% of 4mC modification genes also included alternative splicing events. Finally, we investigated cellulose, hemicellulose, and lignin-related genes, which were associated with secondary growth and contained different DNA modifications. The high-quality genome sequence and annotation of C. equisetifolia in this study provide a valuable resource to strengthen our understanding of the diverse traits of trees.

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“…Among them, the positive sequences of Drosophila, Tolypocladium and yeast were downloaded from the MethSMRT [29] database (http://sysbio.sysu.edu.cn/methsmrt/), and the sequences described as "6mA"were deemed as the 6mA positive sequences. The positive sequences of Rice indica were derived from the eRice websites (http://www.elabcaas.cn/rice/downloads.html), while those of Arabidopsis thaliana [9] were collected from the NCBI Gene Expression Omnibus (GEO) with accession number GSE81596 (GSM2157793), and those of Fragaria vesca [30], and Rosa chinensis [31] were obtained from the MDR database (http://mdr.xieslab.org/).…”

Section: Including Arabidopsis Thaliana Fragaria Vesca Rosa Chinementioning

confidence: 99%

SICD6mA: Identifying 6mA Sites using Deep Memory Network

Liu

2020

Preprint

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Background:DNA N6-methyladenine (6mA) is a kind of epigenetic modification in prokaryotes and eukaryotes, which involves multiple biological processes, such as gene regulation and tumorigenesis. Identifying 6mA contributes to understand its regulatory role. Therefore, to satisfy the needs of large-scale preliminary screening, it is necessary to develop the high-quality computational models for the rapid identification of 6mA sites. However, the existing calculation approaches are mostly specific to rice, and they have not been extensively applied to human genome. Results:This study proposed a classification method of deep learning based on the memory mechanism namedSICD6mA. In addition, the large benchmark datasets were constructed for human and rice, respectively, which integrated the recently reported 6mA sites. According to the evaluation results, SICD6mA displayed favorable robustness during cross-validations, which achieved the area under the curve (AUC) values of 0.9824 and 0.9903 for Human and Rice's genomes in independent test evaluations, separately. Conclusions:The successful prediction rate of 6mA sites on cross-species genomes exhibited higher accuracy than that of the state-of-the-art methods. For the convenience of experimental scientists, the user-friendly tool SICD6mA was developed to predict the cross-species 6mA sites, thereby accelerating and facilitating future cross-species genome research. BackgroundDNA N6-methyladenine(6mA) refers to methylation at the N6site of adenine[1]. Typically, DNA 6mA modification is the most common DNA modification in prokaryotic genomes[2], which is once thought not to exist in eukaryotes[3] (including humans), because it is not detected in earlier studies. With the development of high-throughput sequencing technology, numerous 6mA modifications have been detected in different multicellular eukaryotes. In recent years, 6mA modification has been found to play an important role in DNA epigenetic modification of eukaryotes. DNA methylation represents a key element in epigenetic regulation, and DNA 6mA modification exerts a vital part in regulating gene expression[4], germ cell differentiation[5] etc. It has been reported in the genomes of E. coli[6], Drosophila melanogaster[7], rice[8], and Arabidopsis[9] etc.Currently, the 6mA sites can be detected in mouse and human cells using the sensitive detection technology. 6mA

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DNA N6-adenine methylation in Arabidopsis thaliana

Cited by 20 publications

References 0 publications

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth

SICD6mA: Identifying 6mA Sites using Deep Memory Network

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