RNA modification database explained
This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs.[1] [2] [3] More than 100 different types of RNA modifications have been characterized across all living organisms. It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases.[1] [2] [3] [4]
RNA Modification Databases
| Name | Description | type | Link | References |
|---|
| RMBase | RMBase is designed for decoding the landscape of RNA modifications identified from high-throughput sequencing data (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). It demonstrated thousands of RNA modifications located within mRNAs, regulatory ncRNAs (e.g. lncRNAs, miRNAs), miRNA target sites, RNA-Binding Proteins (RBPs) Binding sites and disease-related SNPs. | database | website | [5] |
| MODOMICS | MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. | database | website | [6] |
| RNAmods | RNAmods serves as a focal point for information pertaining to naturally occurring RNA modifications | database | website | [7] |
| . | |
Notes and References
- Li. S. Mason. CE. The pivotal regulatory landscape of RNA modifications.. Annual Review of Genomics and Human Genetics. 2013. 15. 127–50. 24898039. 10.1146/annurev-genom-090413-025405. free.
- Song. CX. Yi. C. He. C. Mapping recently identified nucleotide variants in the genome and transcriptome.. Nature Biotechnology. October 2012. 30. 11. 1107–16. 23138310. 10.1038/nbt.2398. 3537840.
- Meyer. KD. Jaffrey. SR. The dynamic epitranscriptome: N6-methyladenosine and gene expression control.. Nature Reviews Molecular Cell Biology. April 2014. 15. 5. 313–26. 24713629. 10.1038/nrm3785. 4393108.
- Jonkhout. Nicky. Tran. Julia. Smith. Martin Alexander. Schonrock. Nicole. Mattick. John S. Novoa. Eva Maria. The RNA modification landscape in human disease. RNA. 30 August 2017. rna.063503.117. 10.1261/rna.063503.117. 5688997.
- Sun. WJ. Li. JH. Liu. S. Wu. J. Zhou. H. Qu. LH. Yang. JH. RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.. Nucleic Acids Research. 11 October 2015. 26464443. 10.1093/nar/gkv1036. gkv1036. 4702777. 44.
- Machnicka. MA. Milanowska. K. Osman Oglou. O. Purta. E. Kurkowska. M. Olchowik. A. Januszewski. W. Kalinowski. S. Dunin-Horkawicz. S. Rother. KM. Helm. M. Bujnicki. JM. Grosjean. H. MODOMICS: a database of RNA modification pathways--2013 update.. Nucleic Acids Research. December 2012. 41. Database issue. D262-7. 23118484. 10.1093/nar/gks1007. 3531130.
- Cantara. WA. Crain. PF. Rozenski. J. McCloskey. JA. Harris. KA. Zhang. X. Vendeix. FA. Fabris. D. Agris. PF. The RNA Modification Database, RNAMDB: 2011 update.. Nucleic Acids Research. December 2010. 39. Database issue. D195-201. 21071406. 10.1093/nar/gkq1028. 3013656.
