RNA Modifications Database List

RNA modification databases bring together information on a wide range of RNA modifications, support bioinformatics analyses, facilitate functional studies of different genes, and play a key role in the fields of molecular biology and biomedical research. In addition, RNA databases can help us identify disease-related modifications and facilitate the discovery of new biomarkers and therapeutic targets, as well as provide a collaborative platform for interdisciplinary research and improve communication among researchers by integrating and enriching educational resources to stimulate more new insights about RNA modifications. Taken together, these features make the RNA Modification Database an important tool for the study of RNA biology.

Biochemical RNA modification database

RNAMDB

• RNAMDB integrates information on a wide range of RNA modifications, providing detailed data on 109 RNA modifications. Each entry contains the chemical structure, common name and symbol, elemental composition and mass, CA registry number and index name, phylogenetic origin, the type of RNA species in which it is found, and references to structure determinations and syntheses where they were first reported. Two notable additions have also been added to the database: guanosine and 8-methyladenosine. Users can browse the information in the database by different categories (e.g., modification type, RNA type) and perform precise queries based on specific parameters (e.g., modification type, site, etc.) to quickly find the information they need, and the database provides a comprehensive view of each modification. In addition, users can download RNA modification data of interest in a variety of formats for subsequent analysis and research.

MODOMICS

• The MODOMICS database is a comprehensive information platform providing detailed information on known RNA modifications, including modifications associated with different RNA molecules (e.g., mRNA, tRNA, rRNA, etc.) The MODOMICS database provides detailed information related to RNA modification, including enzymes that synthesise and modify RNA residues, and their roles in the modification pathway, covering names of key enzymes, guide RNAs and other related proteins involved in the modification process. The MODOMICS database provides detailed information related to RNA modification, including the enzymes that synthesise and modify RNA residues and their role in the modification pathway, and covers the names of key enzymes, guide RNAs, and other relevant proteins involved in the modification process. The database provides information on RNA sequences associated with different RNA modifications, while MODOMICS has created an efficient catalogue to ensure that users can find relevant information quickly. The database also has an extensive Modified RNA Residues Catalogue, listing over 150 different RNA modifications, with each entry including a structural diagram, chemical properties and specific sequence. In addition, MODOMICS explores the association of RNA modifications with a wide range of diseases, revealing how specific modifications affect pathophysiology. It also has an advanced annotation system that categorises the reliability and nature of the data, making it easy for us to search and use.odifications, and researchers can use these sequence backgrounds to design experiments.

A comprehensive database of reversible RNA modifications

MeT-DB v2.0

• The MeT-DB V2.0 database is a resource-specific database dedicated to elucidating the function of N6-methyladenosine (m6A) methylation in RNA modification. The database contains m6A modification data for seven species including human, mouse, Drosophila, zebrafish, pig, Arabidopsis thaliana, and Saccharomyces cerevisiae by integrating sequencing data from 185 samples sequenced from multiple studies to integrate the m6A modification peaks and modification sites for retrieval of their functions. The m6A modification sites were searched through this database: (by samples, by m6A peaks, not suitable for single-base m6A sites), and the database also collects target information related to m6A readers, erasers and writers. The results of m6A analyses retrieved from this database can be cross-analysed with other databases to obtain more information. There are also a series of tools in the database specifically designed for understanding m6A functions, which facilitate the retrieval of information.

RMBase v3.0

• RMBase v3.0 is a comprehensive database that comprehensively analyses the mechanisms of 73 RNA modifications in 62 species including mammals, plants, bacteria, fungi and viruses.RMBase v3.0 integrates 1,880 high-throughput transcriptome sequencing data, and expands the types of RNA modifications such as the addition of m7g, ac4c, and RNA editing as compared to previous ones. The database systematically investigates the regulatory relationship between snoRNA and RNA modifications, reveals the potential co-localisation of histone modifications with RNA modifications, and for the first time explores the dysregulation of expression and mutational mapping of RNA-modified proteins in tumours, as well as providing the function of RNA secondary structure in the vicinity of RNA-modified sites.RMBase v3.0 also provides information on the relationship between RNA modifications and RNA binding protein (RBP), miRNA targets, and other interactors with in-depth analyses. The 'modGeneTool' web tool makes it easy to explore the modification profiles of specific genes or transcripts. In summary, RMBase v3.0 provides eight modules covering transcriptome-wide RNA modification data, allowing us to easily retrieve the information we need.

The workflow of RMBase v3.0(Xuan J et al., 2024)

m6A-Atlas V2.0

• The m6A-Atlas v2.0 database covers a total of 797,091 reliable m6A sites and two single-cell m6A profiles obtained from 13 high-resolution technologies. More than 16 million m6A-enriched peaks were integrated from 2,712 MeRIP-seq experiments using multiple methods, spanning 651 conditions across 42 species including animals, plants, prokaryotes, protists, fungi, and viruses, and quality control of the MeRIP-seq samples was performed so that we could efficiently filter the results according to the quality control metrics to select reliable peaks. The database also has a quality control for m6 In addition, the database annotates various genomic features of the m6A transcriptome, interactions with RNA-binding proteins and microRNAs, potential co-splicing events, and single nucleotide polymorphisms. The database facilitates the exploration of the relationship between m6A and other transcriptomic markers, especially in the regulation of gene expression and disease pathogenesis.

m7GHub V2.0

• m7GHub v.2.0 is a database focusing on the presentation of m7G RNA modification sites, integrating studies from NGS and ONT, and collecting 430,898 identified m7G sites in 23 species including human, mouse and zebrafish. The database contains four modules: m7GDB, m7GDiseaseDB, m7GFinder, and m7GSNPer. m7GDB contains 258,206 validated m7G loci and 172,692 pseudo-loci with detailed functional annotations by different analytical techniques. m7GDiseaseDB, on the other hand, contains 156,206 m7G-associated variants in 3,238 diseases, with detailed SNP annotations and visualisation of the distribution of m7G-SNPs across the genome. m7GFinder and m7GSNPer are two modules that allow us to upload our own RNA sequences or SNP data for accurate m7G locus prediction and association analysis.

REPIC

• The REPIC database brings together m6A-seq and MeRIP-seq data from 672 samples obtained from 61 cell lines or tissues from 11 organisms, allowing us to query m6A modifications in specific cell lines or tissues. In addition, the database adds hundreds of epigenomic arrays to the built-in genome browser integrating 1418 histone chip-seq and 118 DNase-seq data, facilitating us to study m6A modifications and their potential interactions with histone marks and chromatin accessibility.The database integrates m6A modification data and epigenome sequencing data from different species, facilitating our assessment of different types of methylation modifications.

Specialized Reversible RNA Modification Database

CVm6A

• The CVm6A database focuses on a visual database of m6A methylation modifications in different cell lines. The database collects MeRIP-Seq and m6A-CLIP-Seq data from 23 human and 8 mouse cell lines, and systematically analyses the overall pattern of m6A in these cell lines, such as the distribution and abundance of m6A modifications on different RNAs, in different subcellular locations, or on different genes. And the database also integrates m6A modifications in cancer and non-cancer cell lines, which facilitates disease-associated queries.

RMVar

• The RMVar database contains RNA modification loci containing multiple classes of RNA modification sites, elucidating information on functional variants related to RNA modification, specifically the type, location, and RNA molecules (e.g., mRNAs, lncRNAs, etc.) affected by the variants, and the database integrates interactions between RNA-RNA-binding proteins, RNA-RNA interactions, and splicing of RNAs, among others. It also provides associations between RNA variants and diseases, giving us a better understanding of the function of RNA modification variants.

RMDisease

• RMDisease is a genetic variant database for the systematic elucidation of disease-associated variants and their associations with epitranscriptomic disturbances of multiple RNA modification types that integrates RNA modification loci from 68 high-throughput sequencing experiments generated by 18 base-resolution technologies and identifies SNPs that may influence the eight most common RNA modifications.The site supports Customers can search for related diseases and traits by species of interest or directly search for diseases and traits of interest to obtain information about them.

RNA editing database

DARNED

• DARNED is an RNA editing database that integrates published RNA editing data to locate editing sites including A to I in the human, mouse and fly transcriptomes. In addition to the common A to I editing information, some C to U editing sites are also included. It is linked to Wikipedia annotations and provides sequence-based searches as well as region-based searches via Blast.

RADAR

• RADAR, a strictly annotated A to I RNA editing database, contains RNA editing events from a wide range of species including human, mouse, Drosophila, and plants, and supports cross-species comparative studies. It also provides detailed biological annotations as well as detailed query and visualisation functions, including information on the tissue-specific editing level of each editing site, the editing sequence, the site and its possible functions.

For a more in-depth understanding of RNA Modifications, refer to "Overview of RNA Modifications."

References:

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7. Wang X, Zhang Y, Chen K, Liang Z, Ma J, Xia R, de Magalhães JP, Rigden DJ, Meng J, Song B. "m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m7G) epitranscriptome."Nucleic Acids Res.2024;52(D1):D203-D212.https://pubmed.ncbi.nlm.nih.gov/37811871/
8. Liu S, Zhu A, He C, Chen M."REPIC: a database for exploring the N6-methyladenosine methylome."Genome Biol.2020;21(1):100.https://pubmed.ncbi.nlm.nih.gov/32345346/
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10. Huang Y, Zhang L, Mu W, Zheng M, Bao X, Li H, Luo X, Ren J, Zuo Z."RMVar 2.0: an updated database of functional variants in RNA modifications."Nucleic Acids Res.2024:gkae924.https://pubmed.ncbi.nlm.nih.gov/39436017/
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