“…In the case of barley, this database describes only 10 modifications of tRNA and 10 modifications of mRNA, and there is no mention of m 6 A among them, indicating an incomplete data set, so far. Furthermore, numerous unique bioinformatic tools, such m 6 a boost and DeepPromise, have been created to look for and identify the RRACH motif surrounding m6A methylation sites in mammals, while crop species have only one weakly supervised model: m 6 A-Maize, for computational identification of m 6 A-containing regions in plants, based on high-throughput sequencing analysis and results ( Liang et al., 2022 ).…”
Section: Discussion: Modification Of M
6
a Rna And...mentioning
Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.
“…In the case of barley, this database describes only 10 modifications of tRNA and 10 modifications of mRNA, and there is no mention of m 6 A among them, indicating an incomplete data set, so far. Furthermore, numerous unique bioinformatic tools, such m 6 a boost and DeepPromise, have been created to look for and identify the RRACH motif surrounding m6A methylation sites in mammals, while crop species have only one weakly supervised model: m 6 A-Maize, for computational identification of m 6 A-containing regions in plants, based on high-throughput sequencing analysis and results ( Liang et al., 2022 ).…”
Section: Discussion: Modification Of M
6
a Rna And...mentioning
Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.
The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m
6
A sites, in particular full-transcriptome m
6
A. And individual m
6
A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m
6
A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m
6
A methylation, including the experimental detection of m
6
A methylation sites, techniques of data analysis, the way of predicting m
6
A methylation sites, m
6
A methylation databases, and detection of m
6
A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.
“…To date, more than 120 computational approaches have been developed for the computational identification of RNA modifications [21, 22] from the primary RNA sequences. These include the iRNA toolkits [23–31], MultiRM [32], DeepPromise [22], RNAm5CPred [33], SRAMP [11], Gene2vec [34], PEA [35], PPUS [36], WHISTLE [37], m5UPred [38], WeakRM frameworks [39, 40], m6ABoost [41], PULSE [42], m6AmPred [43], BERMP [44] and MASS [45]. Together, these efforts greatly advanced our understanding of multiple RNA modifications at different RNA regions and in various species (see recent reviews [22, 46–48]).…”
Section: Introductionmentioning
confidence: 99%
“…MultiRM [32], DeepPromise [22], RNAm5CPred [33], SRAMP [11], Gene2vec [34], PEA [35], PPUS [36], WHISTLE [37], m5UPred [38], WeakRM frameworks [39,40], m6ABoost [41], PULSE [42], m6AmPred [43], BERMP [44] and MASS [45]. Together, these efforts greatly advanced our understanding of multiple RNA modifications at different RNA regions and in various species (see recent reviews [22,[46][47][48]).…”
As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform m6A-TSHub for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB: a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder: a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar: a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modification; and (4) m6A-CAVar: a database of 587,983 TCGA cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and genetic factor of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at: www.xjtlu.edu.cn/biologicalsciences/m6ats.
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