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Opinion Volume 7 Issue 1
The art of Epitranscriptomics
Dito Anurogo1,2,3
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1International PhD Program for Cell therapy and regeneration medicine (IPCTRM), College of medicine, Taipei medical university (TMU), Taiwan
2Faculty of medicine and health sciences, Universitas muhammadiyah makassar, Indonesia
3School of life institute (SLI), Indonesia
Correspondence: Dito anurogo, International PhD program for cell therapy and regeneration medicine (IPCTRM), College of medicine, Taipei medical university (TMU), Taiwan
Received: January 03, 2022 | Published: January 23, 2022
Citation: Anurogo D. The art of Epitranscriptomics. Int Phys Med Rehab J. 2022;7(1):12. DOI: 10.15406/ipmrj.2022.07.00295
Introduction
Epitranscriptomics is a branch of science from epigenetics that studies the various roles and regulations of RNA, such as: RNA editing, RNA modification, and regulation of noncoding RNA. In short, epitranscriptomics is RNA epigenetics.1,2
Modification of RNA turned out to be beyond the expectations of scientists. Moreover, after the systematic constellation between next-generation sequencing (NGS), antibody immunoprecipitation, and medication.3
Some of the advantages of this reversible RNA modification can be felt in several ways, such as: playing an important role in the regulation of cellular fate determination, sex determination, differentiation, and other benefits.4
The ability of the researchers to create genome-wide maps to understand 95% of RNA modifications is currently very limited by the lack of available selective antibodies and medications.5
The third generation sequencing platform, for example: Oxford Nanopore Technologies (ONT), has successfully laid a fundamental foundation for epitranscriptomics.6
Scientists have benefited from ONTs, for example in the identification of new isoforms, direct identification of modified RNA and DNA, accurate transcriptome profiling, estimation of the 3′ poly(A) tail length, and studies of structural variation within various genomes.7,8
In addition, this ONT technology allows direct measurement of RNA and DNA molecules without prior amplification or fragmentation, thereby not limiting the length of RNA or DNA molecules that can be sequenced.9
Besides being useful for overcoming the limitations of the short-read sequencing process, this ONT technology platform can also directly measure the modifications of RNA and DNA in their native molecules.10
ONT is indeed able to overcome various problems that have not been solved by NGS technology. However, ONT also has limitations, namely the lack of standardized pipelines to carry out the ONT output analysis process. This limits the reach of the ONT to the rest of the scientific community.11
Acknowledgments
None.
Conflicts of interest
The authors have no conflicts of interest to declare.
Funding
None.
References
- Li X, J Peng, C Yi. The epitranscriptome of small non-coding RNAs. Non-coding RNA Research. 2021.
- Song H, Dongcheng Liu, Shaowei Donget, et al. Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications. Signal Transduction and Targeted Therapy. 2020;5(1):193.
- Rouet R, Katherine J L Jackson, David B Langley, et al. Next-Generation Sequencing of Antibody Display Repertoires. Front Immunol. 2018;9:118.
- Frye M, Bryan T Harada, Mikaela Behmet, et al. RNA modifications modulate gene expression during development. 2018;361(6409):1346–1349.
- Liu H, Oguzhan Begik, Morghan C Lucaset, et al. Accurate detection of m6A RNA modifications in native RNA sequences. Nature Communications. 2019;10(1):4079.
- Cozzuto L, Huanle Liu1, Leszek P, et al. Master Of Pores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets. Frontiers in Genetics. 2020;11(211).
- Parker MT, Katarzyna Knop, Anna V Sherwood et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification. eLife. 2020;9:e49658.
- Wang Y, Yuru Wang, Kin Fai Au, et al. Nanopore sequencing technology, bioinformatics and applications. Nature biotechnology. 2021;1–18.
- Hwang B, JH Lee, D Bang. Single-cell RNA sequencing technologies and bioinformatics pipelines. Experimental & Molecular Medicine.50(8):1–14.
- Sahlin K, P Medvedev. Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis. Nature Communications. 2021;12(1):2.
- Pereira R, J Oliveira, M Sousa. Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics. Journal of clinical medicine. 2020.9(1):132.
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