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. 2013 Jan;41(Database issue):D262-7.
doi: 10.1093/nar/gks1007. Epub 2012 Oct 30.

MODOMICS: a database of RNA modification pathways--2013 update

Magdalena A Machnicka  1 , Kaja Milanowska, Okan Osman Oglou, Elzbieta Purta, Malgorzata Kurkowska, Anna Olchowik, Witold Januszewski, Sebastian Kalinowski, Stanislaw Dunin-Horkawicz, Kristian M Rother, Mark Helm, Janusz M Bujnicki, Henri Grosjean
Affiliations

MODOMICS: a database of RNA modification pathways--2013 update

Magdalena A Machnicka et al. Nucleic Acids Res. 2013 Jan.

Abstract

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. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5'-end capping process, and a catalogue of 'building blocks' for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.

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Figures

Figure 1.
Figure 1.
The diversity of chemical groups introduced enzymatically during the process of RNA maturation at various locations of the four common ribonucleosides A, G, C and U linked via 5′- to 3′-phosphodiester bonds. Only conventional acronyms/symbols are shown. The complete scientific names of all modified nucleosides presented in this figure are provided in the MODOMICS database. Nucleosides in RNA can also be doubly or triply modified by the introduction of several of these chemical groups.
See this image and copyright information in PMC

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References

    1. Grosjean H. Nucleic acids are not boring long polymers of only four types of nucleotides: a guided tour. In: Grosjean H, editor. DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution. Austin: Landes Bioscience; 2009. pp. 1–18.
    1. Iwata-Reuyl D. An embarrassment of riches: the enzymology of RNA modification. Curr. Opin. Chem. Biol. 2008;12:126–133. - PMC - PubMed
    1. Ahola T, Kaariainen L. Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP. Proc. Natl Acad. Sci. USA. 1995;92:507–511. - PMC - PubMed
    1. Globisch D, Pearson D, Hienzsch A, Bruckl T, Wagner M, Thoma I, Thumbs P, Reiter V, Kneuttinger AC, Muller M, et al. Systems-based analysis of modified tRNA bases. Angew Chem. Int. Ed. Engl. 2011;50:9739–9742. - PubMed
    1. Montgomery TA, Rim YS, Zhang C, Dowen RH, Phillips CM, Fischer SE, Ruvkun G. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLoS Genet. 2012;8:e1002616. - PMC - PubMed

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