The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.
Decoding the epitranscriptional landscape from native RNA sequences
Open accessAbstract
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
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Metadata
- Authors
- Jenjaroenpun, P., Wongsurawat, T., Wadley, T. D., Wassenaar, T. M., Liu, J., Dai, Q., Wanchai, V., Akel, N. S., Jamshidi-Parsian, A., Franco, A. T., Boysen, G., Jennings, M. L., Ussery, D. W., He, C., & Nookaew, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-07-25
- Volume
- 49
- Issue
- 2
- Pages
- e7-e7
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3043981686
- Cited by
- 282
- References
- 59
- FWCI
- 9.68
- Type
- journal article
- Language
- en
- Open access
- gold
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- Jenjaroenpun, P., Wongsurawat, T., Wadley, T. D., Wassenaar, T. M., Liu, J., Dai, Q., Wanchai, V., Akel, N. S., Jamshidi-Parsian, A., Franco, A. T., Boysen, G., Jennings, M. L., Ussery, D. W., He, C., & Nookaew, I. (2021). Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa620
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