ABSTRACT
The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA and is maintained as an
updated version of the initial printed report. Information provided includes:
type(s) of RNA in which found and phylogenetic distribution; common chemical
names and symbols; Chemical Abstracts registry numbers and index names;
chemical structures; initial literature citations for structural
characterization or occurrence and chemical synthesis. The data are available
through the World Wide Web, anonymous ftp or from the authors in printed form.
Both the structural diversity and extent of post-transcriptional modification in RNA is remarkable, with more than 93
different nucleosides presently known in all types of RNA (
1
). The discovery of new modified nucleosides as well as increasing knowledge of
the array of functional roles of modification, based largely on extensive
studies of tRNA (
2
-
4
), mandates a need for a comprehensive database of RNA nucleosides. The RNA
Modification Database is maintained as an extension of the initial version
published in mid-1994 (
1
). The database consists of all RNA-derived ribonucleosides of known structure, including those from
established sequence positions, as well as those detected or characterized from
hydrolysates of RNA. The information provided permits access to the modified
nucleoside literature through provision of both computer searchable Chemical
Abstracts registry numbers and key literature citations.
The reader is referred to the earlier publication (
1
) or to the text portion of the present database for comments or discussion of
the following topics: usage of modified nucleoside symbols and notations;
accuracy of assignments in the early literature; problems associated with
modification assignments in rRNA; exclusion from the database collection of
nucleoside degradation products and of erroneous structures or distributions in
literature reports.
The authors invite comments concerning new entries, errors or omissions and on
the format presently used for electronic access to the database. The email
address for this purpose is:
rnamods{at}ecclab.med.utah.edu
In general each nucleoside file consists of the following.
Type of RNA in which found: tRNA (presently consisting of 79 nucleosides), rRNA
(28), mRNA (12), snRNA (11), chromosomal RNA (two) and other RNAs (one).
Common chemical names and symbols.
Chemical Abstracts registry numbers for the ribonucleoside and corresponding
base if assigned.
Chemical Abstracts index name, which in some cases includes stereochemical
information not shown in the database chemical structure.
Chemical structure of nucleoside.
Phylogenetic occurrence of the RNA in which found, archaea (archaebacteria),
(eu)bacteria or eukarya, and the corresponding literature citations for each.
Ribosomal RNA entries are further distinguished by RNA size, e.g. 16S, 28S.
Literature citation to structure assignment of the nucleoside.
Literature citation to the first reported chemical synthesis of the nucleoside
or, in limited cases, of the base. Subsequent reports of synthesis, which often
include refinements, can be accessed effectively by computer through the
Chemical Abstracts registry numbers.
Comments on any of the above entries, including additional literature citations
or alternative nomenclature.
Access to individual nucleoside files within the database can be made through
any of four entry points: common name; abbreviation symbol; RNA type; chemical
structure (displayed graphically via WWW format). An example of the information
contained in a single nucleoside file is shown in Figure
1
.
The database currently (October, 1995) contains 94 modified ribonucleoside
entries, distributed by RNA type and phylogenetic source as shown in Table
1
.
Starting in late 1995 the modification database will be accessible as follows:
anonymous ftp (ftp://medlib.med.utah.edu/library/RNAmods);
World Wide Web (http://www-medlib.med.utah.edu/RNAmods/RNAmods.html);
in printed form from either author at 311A Skaggs Hall, University of Utah, Salt
Lake City, UT 84112, USA (email rnamods@ecclab.med.utah.edu).
Table 1
We are grateful to Y. Zhang, S. C. Pomerantz and N. Lombardo for assistance in
implementing the electronic version of the database. Maintenance of the
database is supported by NIH grant GM 29812.
RNA
Source
Archaea
(eu)Bacteria
Eukarya
tRNA
36
42
46
rRNA
1
a
4
a
SSU
3
8
18
LSU
14
12
5S
3
1
5.8S
5
mRNA
12
snRNA
11
Chromosomal RNA
2
Other small RNA
1
REFERENCES
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