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m6A methylation and forecasting tools summary

Reversibly modified schematic three levels of DNA, RNA and proteins (Fu et al. Nature Reviews Genetics, 2014) DNA and the presence of various protein modifications, RNA is no exception, currently known more than hundreds of RNA modifications. The encoding can be subdivided into RNA encoding RNA (protein-coding RNA) and non-coding RNA (noncoding RNA) into two categories, those that various modifications will occur after RNA transcription, including polyadenylation methylated N6- (N6-methyladenosine , m6A), cytosine hydroxylated (m5C), N1- adenylate methylated (of m1A) and the like. m6A after eukaryotic RNA methylation is the most common form of post-translational modifications, RNA approximately accounted for about 80% of methylation modification.

Eukaryotes, various chemical modifications of mRNA (Roundtree et al. Cell, 2017) m6A methylation and demethylation (A) and the downstream effects on protein-RNA interactions (B) (Roundtree et al. Cell , 2017) in recent years, RNA methylation gradually one of today’s hottest areas of research. Because the function is essential m6A methylation, which is closely related to the abnormal occurrence of various diseases, the development, including tumors or cancer, a variety of neurological disorders, fetal growth retardation. Articles about RNA methylation now presented a growth spurt, many of which are made in the leading journals Nature, Science, Cell and so on. m6A methylation of biological pathways and related functions (Lee et al. Cell, 2014) since m6A methylation has such an important function, and now research is very hot, then we can predict whether the RNA of which sites occur potential m6A methylation of it, and then decide whether it is necessary to continue to do the appropriate experiments to verify it. The answer is yes! Next, we will talk about what software or online tools to predict the potential m6A RNA methylation sites directly from the sequence.

Currently, there are already a number of tools have been developed to predict m6A methylation sites in the RNA, these tools published articles in chronological order according to the main (More exciting please pay attention to micro-channel public number: AIPuFuBio):

1. iRNA-Methyl

Software address: http: //lin.uestc.edu.cn/server/iRNA-Methyl

Published an article: Chen et al iRNA-Methyl:. Identifying N (6) -methyladenosine sites using pseudo nucleotide composition Analytical Biochemistry, 20152 SRAMP..

Software address: http: //www.cuilab.cn/sramp/

Published articles: Zhou et al SRAMP:.. Prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features Nucleic Acids Research, 20163. iRNAm5C-PseDNC

Software address: http: //www.jci-bioinfo.cn/iRNAm5C-PseDNC

Published an article: Qiu et al iRNAm5C-PseDNC:.. Identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition Oncotarget, 20174. M6AMRFS

Software address: http: //server.malab.cn/M6AMRFS/

Published an article: Qiang et al M6AMRFS:.. Robust Prediction of N6-Methyladenosine Sites With Sequence-Based Features in Multiple Species Frontiers in Genetics, 20185. M6APred-EL

Software address: http: //server.malab.cn/M6APred-EL/

Published an article: Wei et al M6APred-EL:. A Sequence-Based Predictor for Identifying N6-methyladenosine Sites Using Ensemble Learning Molecular Therapy:. Nucleic Acids, 20186. DeepM6ASeq

Software address: https: //github.com/rreybeyb/DeepM6ASeq

Published an article:. Zhang et al DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning BMC Genomics, 2018.

 

Above these software can predict m6A methylation sites in the RNA, then how to further comment m6A methylation functions? Specific tools are available as follows:

Software name: m6Acomet

Software address: http: //www.xjtlu.edu.cn/biologicalsciences/m6acomet

Published an article: Wu et al m6Acomet:.. Large-scale functional prediction of individual m6 A RNA methylation sites from an RNA comethylation network BMC Bioinformatics, 2019

 

So, if we are interested in a certain article or RNA, just find the corresponding RNA nucleotide sequence, RNA sequence can be predicted potential methylation sites m6A of 6 using the software referred to herein. If further forecasting m6A methylation sites can be controlled through software, such as m6Acomet. The software may allow the user in a large-scale prediction m6A RNA methylation sites, to overcome the disadvantages and to verify the experiment only a small amount of RNA sequences. Moreover, the software predicted results, you can further narrow the scope of experimental verification, saving research time and reduce the risk of failed experiments. (More exciting, we can see a large free integrated bioinformatics tools and resources platform AIPuFu: www.aipufu.com, focus on micro-channel public number: AIPuFuBio). We hope that today’s content to be useful, will continue to update the classic content, welcome message ~ ~ References

1. Fu et al. Gene expression regulation mediated through reversible m⁶A RNA methylation, Nature Reviews Genetics, 2014

2. Roundtree et al. Dynamic RNA Modifications in Gene Expression Regulation, Cell, 2017

3. Lee et al. Emerging Roles of RNA Modification: m6 A and U-Tail, Cell, 2017

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