Abstract
Over 100 types of chemical modifications have been identified in protein-coding and noncoding RNAs (ncRNAs). However, the prevalence, regulation, and function of diverse RNA modifications remain largely unknown. In this chapter, we describe how to annotate, visualize, and analyze the RNA modification sites from the high-throughput epitranscriptome sequencing data using RMBase platform and software. We developed two stand-alone computational software, modAnnotator and metaProfile, to annotate and visualize RNA modification sites and their prevalence in the gene body. In addition, we constructed interactive web implementations to decode the atlas of various RNA modifications, including the N6-methyladenosine (m6A) modification, pseudouridine (Ψ) modification, 5-methylcytosine (m5C) modification, and 2′-O-methylation (2′-O-Me) modification, as well as other types of modifications. We also developed web-based interfaces to analyze the associations between RNA modification sites with miRNA target sites and disease-related single-nucleotide polymorphisms (SNPs). Moreover, RMBase provides a genome browser and a web-based modTool to query, annotate, and visualize various RNA modifications. RMBase is expected to provide comprehensive interfaces and tools to facilitate the analysis and functional study of the massive RNA modification sites. The software and platform are available at http://rna.sysu.edu.cn/rmbase/modSoftware.php.
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Acknowledgments
This research is supported by National Key R&D Program of China (2017YFA0504400). National Natural Science Foundation of China (91440110, 31770879, 31370791, and 81702945); the funds from Guangdong Province (2017A030313106 and 2017A030313483); The project of Science and Technology New Star in ZhuJiang Guangzhou city (No. 2012J2200025); Fundamental Research Funds for the Central Universities (2011330003161070, 14lgjc18,2017MS071); Seeding project fund at School of Medicine, South China University of Technology (yxy2016005). Guangdong Province Key Laboratory of Computational Science and the Guangdong Province Computational Science Innovative Research Team.
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Zhang, XQ., Yang, JH. (2019). Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data. In: Wajapeyee, N., Gupta, R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8808-2_8
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DOI: https://doi.org/10.1007/978-1-4939-8808-2_8
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