Overview

The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report [1].

The chemical composition of an RNA molecule allows for its inherent ability to play many roles within biological systems. This ability is further enhanced through the site selected addition of the 109 currently known post-transcriptional modifications catalyzed by specific RNA modification enzymes [2]. These naturally-occurring modifications are found in all three major RNA species (tRNA, mRNA and rRNA) in all three primary phylogenetic domains (archaea, bacteria and eukarya) as well as in a handful of other RNA species such as snRNA and miRNA [3,4,5,6]. Both the chemical and structural diversity and extent of posttranscriptional modification in RNA is remarkable [1,7,8,9], with 109 different modified nucleosides presently known. The modifications are one of the most evolutionarily conserved properties of RNAs. Due in large part to comprehensive investigations into the structural and functional roles of modified nucleosides in tRNA, significant advancements have been achieved in our understanding of the various roles played by these modifications [6,10,11,12,13,14]. The need to provide a comprehensive, searchable database to house this wealth of knowledge led to the first iteration of The RNA Modification Database (RNAMDB) in 1994 [1].

The current version of the database, now housed at The RNA Institute at the State University of New York at Albany, contains all naturally-occurring, RNA-derived modified ribonucleosides for which the chemical structures are known. They include those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The RNAMDB provides a user-friendly, searchable interface that directs the user to a detailed information page for each database entry. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations.

This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. The reader is referred to the earlier publication [1] and to paragraphs below for discussion of selected topics relevant to the database.

Users are invited to submit comments regarding existing entries, including errors and omissions, as well as suggestions for improvements to the following email address: rnamdb@albany.edu.

  • Comments on usage of nucleoside symbols

    In general, the symbol "N" is preferred for modified nucleosides of unknown structure, or "Nm" if ribose methylation of O-2' has been established. If the heterocyclic moiety is known or assumed, for example from the corresponding gene sequence, the designation A*, U*, etc. is recommended. The use of "X" for an unknown nucleoside is not recommended because of confusion with the nucleoside acp3U (see comment in the acp3U file). The superscript "x" is useful to indicate a form of modification without designation of position; for example "mxC" for cytidine monomethylated in the base at an unknown or unspecified position. Likewise "x" is sometimes used in the fashion "x5s2U", as to generically designate 5-substituted derivatives of 2-thiouridine. The use of "m" for "modified", as in "mA" (occasionally used in the rRNA literature) is strongly discouraged because of the ambiguity associated with use of simply "m" for methylation.

    Additional comments are found under Symbol in the Description of Entries section.

  • Accuracy of assignments in the early literature

    Entries in each file are categorized by type of RNA, although in early work total cellular RNA was often isolated with no clear distinction made between tRNA ("soluble RNA"), the various rRNAs ("microsomal") or others. In such cases the listing given in the database may correspond to contemporary knowledge of distribution of the nucleoside within certain types of RNA. Some of the earlier literature concerning modification in rRNA is of questionable accuracy, and this particular problem is addressed in the next section ("Nucleoside modification in ribosomal RNA").

  • Modifications excluded from the database

    Excluded from the database are those modifications known to be artifactual, for example as a consequence of degradation, or those having clearly incorrect chemical structures. If the basis of structure assignment or identification is considered to be inconclusive, this is indicated under Comments in individual files.

    There are several notable examples of modifications that have not been included in the compilation.

    • The covalently bonded adduct between the tRNA nucleoside N6-threonylcarbamoyladenosine (t6A) and the base Tris, is a complex nucleoside isolated and characterized from E.coli tRNA [15] (Chemical Abstracts registry number 61172-4-6), and is presently believed to be formed in vitro during tRNA isolation [15], and is thus not a fully natural nucleoside.
    • Second, posttranscriptional methylation in some small nuclear RNAs results in a 5'-CH3pppN... structure, rather than the more common m2,2,7GpppN... cap in which the terminus is a nucleoside [16].

    In addition, entries have not been made for natural modified nucleosides that have been only partially characterized. Several examples are as follows:

    • An unknown E. coli tRNA nucleoside, initially discovered by S. Yokoyama [17] Tokyo University, designated t6A* with unmodified ribose; Mr 412, elutes before or concominent with adenosine in RPHPLC.
    • An unknown modified C was reported in E. coli 23S rRNA in very low amounts at position 2501, corresponding in mass to C plus net addition of 16 daltons [18].
    • A new derivative of 5-methylaminomethyl-2-thiouridine (mnm5s2U), in which a C10H17 side chain of unknown structure is attached to S-2 [19].
    • An unusual derivative of cytidine, designated N-330, was sequenced to position 1404 in SSU rRNA of the bacterium Thermotoga maritima; Mr 330.117, tr (HPLC) 3.7 min, with unmodified ribose [20].

  • Some other listings and reviews of RNA modification
    • general distribution of modifications in RNA [9]
    • distribution of modifications in tRNA by sequence position [21]
    • tRNA gene sequences [22]
    • mitochondrial tRNA [24]
    • archaeal tRNA [25]
    • eukaryotic mRNA [26]
    • eukaryotic rRNA [28]
    • distribution of pseudouridine in rRNA [31]
    • rRNA, influence of modification [32]
    • small subunit rRNA database [4]
    • mRNA cap structures [34]
    • small nuclear RNA [37]
    • nucleolar "guide" RNAs [35]
    • biophysical consequences of modification [39]
    • extensive reviews and general coverage of modification [13]

  • Conclusions

    A total of 109 modified nucleosides for which chemical structures have been assigned have been reported in RNA. The largest number, 93, with the greatest structural diversity, are found in tRNA, with 31 in rRNA, 13 in mRNA and 14 in other RNA species, most notably snRNA. Based on lessons learned primarily from tRNA, it is clear that many modification motifs and their sequence locations tend to be conserved, although distinct differences among the three primary phylogenetic domains are observed.It is clear that present knowledge of the chemical diversity of RNA nucleosides, and certainly of their distribution, is somewhat narrowly confined to relatively few organisms. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings.

    This compilation is maintained as a continuously updated database.Comments concerning format, omissions or newly published material are solicited.

  • References for this overview
  1. Limbach, P.A., Crain, P.F. and McCloskey, J.A. (1994) Summary: the modified nucleosides of RNA. Nucleic Acids Res, 22, pp. 2183-96. PubMed
  2. Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M., Grosjean, H. and Rother, K. (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res, 37, Database issue, D118-D121. PubMed
  3. Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R. and Chen, X. (2005) Methylation as a crucial step in plant microRNA biogenesis. Science, 307, pp. 932-5. PubMed
  4. McCloskey, J.A. and Rozenski, J. (2005) The Small Subunit rRNA Modification Database. Nucleic Acids Res, 33, Database issue, pp. D135-8. PubMed
  5. Rozenski, J., Crain, P.F. and McCloskey, J.A. (1999) The RNA Modification Database: 1999 update. Nucleic Acids Res, 27, Database issue, pp. 196-7. PubMed
  6. Curran, J.F. (1998) In Grosjean, H. and Benne, R. (eds.) Modification and Editing of RNA. ASM Press, Washington D.C., pp. 493-516.
  7. Jühling, F., Mörl, M., Hartmann, R.K., Sprinzl, M., Stadler, P.F. and Pütz, J. (2009) tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res, 37, Database issue, pp. D159-62. PubMed
  8. McCloskey, J.A. (2001) In Söll, D., Nishimura, S. and Moore, P.B. (eds.) RNA. Elsevier, Amsterdam, pp. 309-16.
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  11. Agris, P.F. (2008) Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep, 9, pp. 629-35. PubMed
  12. Agris, P.F., Vendeix, F.A.P. and Graham, W.D. (2007) tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol, 366, pp. 1-13. PubMed
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  14. Yokoyama, S. and Nishimura, S. (1995) In Söll, D. and RajBhandary, U.L. (eds.) tRNA Structure, Biosynthesis and Function. ASM Press, Washington D.C., pp. 207-23.
  15. Kasai, H., Murao, K., Liehr, J.G., Crain, P.F., McCloskey, J.A. and Nishimura, S. (1976) Structure determination of a modified nucleoside isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine. Eur J of Biochem, 69, pp. 435-44. PubMed
  16. Singh, R. and Reddy, R. (1989) Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA. Proc Natl Acad Sci USA, 86, pp. 8280-3. PubMed
  17. Yokoyama, S., Personal communication.
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  19. Chen, P., Crain, P.F., Näsvall, S.J., Pomerantz, S.C. and Björk, G.R. (2005) A "gain of function" mutation in a protein mediates production of novel modified nucleosides. EMBO J, 24, pp. 1842-51. PubMed
  20. Guymon, R., Pomerantz, S.C., Ison, J.N., Crain, P.F. and McCloskey, J.A. (2007) Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine. RNA, 13, pp. 396-403. PubMed
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