DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology

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/.

Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells

“…In our study, the potential m5C sites of RNF126 in the HCT15 cell line were considered in Chromosome 19:663046–663233. This is inconsistent with the conclusions of the previous two public databases ( Ma et al, 2022 ; Zhang et al, 2023 ). This may be the new m5C site of RNF126.…”

“…DirectRMDB ( Zhang et al, 2023 ) and m5C Atlas ( Ma et al, 2022 ) are two public databases that integrate a large number of m5C sequencing results. We compared the predicted m5C modification sites with m5C-Atlas and DirectRMDB to identify novel m5C sites in HCT15/NSUN2KD-HCT15.…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…RM2Target ( 9 ), a development of the earlier m6A2Target database ( 10 ), covers writes, erasers and readers of nine RNA modifications as well as diverse annotations and biomedical implications. The third of the trio, DirectRMDB ( 11 ), collects data from direct RNA sequencing that captures quantitative RNA modifications, annotating the results in an isoform-specific manner. Long ncRNA data are covered in update papers from three popular resources.…”

Epitranscriptomics in the development, functions, and disorders of cancer stem cells

“…Direct RNA sequencing (DRS), commercialized by Oxford Nanopore technologies (ONT), is able to directly detect any given modifications in a single transcript, improving these limitations of NGS-based methods. For example, Zhang et al (189) presented DirectRMDB, the first ONT-based quantitative mapping database of RNA modifications, which includes 16 types and a total of 904,712 modification sites in 25 species from 39 independent studies. This platform integrates three generation sequencing and eight RNA modification detection technologies, making it possible to easily query specific modifications on RNA isomers.…”