期刊
NATURE COMMUNICATIONS
卷 10, 期 -, 页码 -出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-019-11713-9
关键词
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资金
- international PhD fellowship (UIPA) from the University of New South Wales
- CRG International PhD Fellowships Programme
- DECRA fellowship from the Australian Research Council [DE170100506]
- Australian Research Council [DP180103571]
- Spanish Ministry of Economy, Industry and Competitiveness (MEIC)
- Centro de Excelencia Severo Ochoa
- CERCA Programme/Generalitat de Catalunya
- Bert L and N Kuggie Vallee Foundation
- WorldQuant Foundation
- Pershing Square Sohn Cancer Research Alliance
- NASA [NNX14AH50G, NNX17AB26G]
- National Institutes of Health [R01ES021006, 1R21AI129851, 1R01MH117406]
- Bill and Melinda Gates Foundation [OPP1151054]
- Leukemia and Lymphoma Society [LLS 9238-16, LLS-MCL-982]
- CRG Severo Ochoa Funding
- Australian Research Council [DE170100506] Funding Source: Australian Research Council
The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct RNA sequencing, N-6-methyladenosine (m(6)A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Specifically, we find that our algorithm, trained with m(6)A-modified and unmodified synthetic sequences, can predict m(6)A RNA modifications with similar to 90% accuracy. We then extend our findings to yeast data sets, finding that our method can identify m(6)A RNA modifications in vivo with an accuracy of 87%. Moreover, we further validate our method by showing that these 'errors' are typically not observed in yeast ime4-knockout strains, which lack m(6)A modifications. Our results open avenues to investigate the biological roles of RNA modifications in their native RNA context.
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