Zhang, Yuxin, Jiang, Jie, Ma, Jiongming, Wei, Zhen, Wang, Yue, Song, Bowen, Meng, Jia 
ORCID: 0000-0003-3455-205X, Jia, Guifang, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 2 more authors)
(2022)
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Nucleic acids research, 51 (D1).
gkac1061-gkac1061.
Abstract
With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http://www.rnamd.org/directRMDB/.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Protein Isoforms, RNA, Sequence Analysis, RNA, RNA Processing, Post-Transcriptional, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing |
| Divisions: | Faculty of Health and Life Sciences Faculty of Science and Engineering > School of Electrical Engineering, Electronics and Computer Science Faculty of Health and Life Sciences > Institute of Life Courses and Medical Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 21 Nov 2022 09:13 |
| Last Modified: | 28 Jan 2023 08:52 |
| DOI: | 10.1093/nar/gkac1061 |
| Open Access URL: | https://academic.oup.com/nar/advance-article/doi/1... |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3166290 |
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