TY - JOUR
T1 - DirectRMDB
T2 - a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology
AU - Zhang, Yuxin
AU - Jiang, Jie
AU - Ma, Jiongming
AU - Wei, Zhen
AU - Wang, Yue
AU - Song, Bowen
AU - Meng, Jia
AU - Jia, Guifang
AU - De Magalhães, João Pedro
AU - Rigden, Daniel J.
AU - Hang, Daiyun
AU - Chen, Kunqi
N1 - Funding Information:
FUNDING National Natural Science Foundation of China [32100519 and 31671373]; XJTLU Key Program Special Fund [KSFE- 51 and KSF-P-02]; Scientific Research Foundation for Advanced Talents of Fujian Medical University [XRCZX202109]. Funding for open access charge: Scientific Research Foundation for Advanced Talents of Fujian Medical University [XRCZX202109].
Publisher Copyright:
© 2023 The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2023/1/6
Y1 - 2023/1/6
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=85144700998&partnerID=8YFLogxK
U2 - 10.1093/nar/gkac1061
DO - 10.1093/nar/gkac1061
M3 - Article
C2 - 36382409
AN - SCOPUS:85144700998
SN - 0305-1048
VL - 51
SP - D106-D116
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -