MODOMICS: a database of RNA modification pathways. 2021 update

Abstract

The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5′-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…The various relationships between TFs and cell markers are described in the new database TF-Marker ( 23 ), and the same group also describe TcoFBbase ( 24 ) covering transcription cofactors and associated regulatory networks. Elsewhere, notable returning databases include MODOMICS ( 25 ) which now links to PDB structures containing modified RNA and has improved associations between RNA modification and disease; miRTarBase ( 26 ) which updates content significantly and includes new features such as editing and disease-related variants; and miRNATissueAtlas ( 27 ) which switches from microarray-based analysis to deep sequencing and expands the number of donors and tissues to give a higher resolution picture of the tissue specificity of miRNA expression.…”

Research Progress of RNA Methylation Modification in Colorectal Cancer

“…RNA modifications play a key regulatory role in gene expression ( Helm and Motorin, 2017 ; Wu et al, 2021 ). In recent years, over 170 RNA chemical modifications have been discovered, involving both coding and noncoding RNAs ( Boccaletto et al, 2022 ). In eukaryotic, the most abundant modification found is N6-methyladenosine (m6A), which is considered as eukaryotic characteristic internal modification since its discovery in the 1870s ( Gilbert et al, 2016 ; Davalos et al, 2018 ).…”

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches

“…Out of the 143 naturally occurring RNA modifications that are currently listed in the Modomics database [ 30 ], 57% contain modifications that affect the Watson–Crick–Franklin (W-C-F) edge, 46% contain modifications that affect the Hoogstein/“C-H” edge, 0.7% contain modifications that affect the backbone (phosphate), and 20% contain modifications that affect the sugar edge. Many RNA modifications have multiple sites modified and are represented as such in the percentages.…”