MODOMICS: a database of RNA modifications and related information. 2023 update

Abstract

The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with 'Evidence' and 'Estimated Reliability' features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

Graphical Abstract

Figure 1.

Illustration of the key new features in MODOMICS. Top panel: Examples of modifications sites identified in rRNAs using high-resolution cryo-EM and fragment-based MS analysis of 80S ribosomes. The modified ribonucleotides are shown in the context of the Coulomb density map displayed as blue mesh, with modifications indicated by red ellipsoids. Below, the validation by mass spectrometry using enzyme-induced RNA fragment analysis is illustrated. Bottom panel: 2D schemes of ribonucleotide residues imported to MODOMICS: 2′-deoxy-2′-(4-ethyl-1H-1,2,3-triazol-1-yl)adenosine 5′-(dihydrogen phosphate), left; [(6-amino-9H-purin-9-yl)-[5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole]-4′yl]methyl dihydrogen phosphate (ANZ), right. Chemical modifications are highlighted in red.