Nucleic Acids Research, 2002, Vol. 30, No. 1 335-340
© 2002 Oxford University Press
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy, 1Centro di Studio sui Mitocondri e Metabolismo Energetico del Consiglio Nazionale delle Ricerche (CNR), via Amendola 165/A, 70126 Bari, Italy and 2Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, via Orabona 4, 70126 Bari, Italy
Received September 21, 2001; Accepted October 2, 2001.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All Internet resources we implemented for retrieval and functional analysis of 5'- and 3'-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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The completion of the sequencing of human and of other organism genomes has opened new avenues for understanding the basic mechanisms of cell function. These processes mostly rely on a spatial–temporal coordinated expression of genes mediated by regulatory elements embedded in the non-coding part of the genomes. Among non-coding regions, the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs have often been experimentally demonstrated to contain sequence elements crucial for many aspects of gene regulation and expression (1–7).
The main functional roles so far demonstrated for 5'- and 3'-UTR sequences are: (i) control of mRNA cellular and subcellular localization (4,7–9); (ii) control of mRNA stability (1,10,11); (iii) control of mRNA translation efficiency (12–14).
Several regulatory signals have already been identified in 5'- or 3'-UTR sequences, usually corresponding to short oligonucleotide tracts, also able to fold in specific secondary structures, which are protein binding sites for various regulatory proteins.
The analysis of large collections of functionally equivalent sequences (15,16), such as 5'- and 3'-UTR sequences, could indeed be very useful for defining their structural and compositional features as well as for searching the alleged function-associated sequence patterns (17–19). For this reason we constructed UTRdb, a specialized sequence collection, deprived from redundancy, of 5'- and 3'-UTR sequences from eukaryotic mRNAs.
UTRdb entries have been enriched with specialized information, not present in the primary databases, including the presence of sequence patterns demonstrated by experimental evidence to play some functional role. Additionally, because 
10% of mammalian mRNAs contain repetitive elements in their UTRs (20) but they are usually not annotated in the original records, we decided to add this information into our database as well.
We also created UTRsite, a collection of functional sequence patterns located in the 5'- or 3'-UTR sequences which could prove very useful for automatic annotation of anonymous sequences generated by sequencing projects as well as for finding previously undetected signals in known gene sequences.
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UTRdb GENERATION |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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The specialized database of UTR sequences was generated by UTRdb_gen, a computer program we devised for this task. Eight sequence collections were generated for both 5'- and 3'-UTR sequences, one for each of the eukaryotic division of the EMBL/GenBank nucleotide database, namely: (i) human, (ii) rodent, (iii) other mammal, (iv) other vertebrate, (v) invertebrate, (vi) plant, (vii) fungi and (viii) virus.
UTRdb_gen, performing an accurate parsing of the Feature Table of the relevant EMBL entries is able to automatically generate the various UTRdb collections. Although the feature keys ‘5'UTR’ and ‘3'UTR’ is a valid feature for the EMBL/GenBank entries, only a small percentage of the entries are adequately annotated. Indeed, of the about 250 000 primary entries where UTRdb_gen was able to extract 5'- or 3'-UTR sequences, only 12% contained the 5'UTR or 3'UTR feature key in the corresponding EMBL entry. UTRdb_gen is able to define UTRs, even when these keys are not reported in the primary entry by using a predefinite syntactic parsing of other relevant feature keys, such as mRNA, CDS, exon, intron, etc.
UTRdb_gen automatically annotates generated UTR entries by adding some specialized information such as completeness or incompleteness of the UTR, number of spanned exons and cross-referencing to the primary database entry. A cross reference between 5'- and 3'-UTR sequences from the same mRNA has also been established.
A further interface between the UTRdb_gen and the BLAST engine (parameters: expect < 10–5, minimum length = 50 nt, percentage identity > 95%) adds information about the position and the identity of any vector that may contaminate UTR entries.
The generation of UTR entries cleaned from redundancy has been obtained by using CLEANUP program (21) which is able to generate automatically, and very quickly, cleaned collections by removing entries that have a similarity and overlapping degree with longer entries present in the database above a user-fixed threshold. In this case, the cut-off parameters we used for the CLEANUP application were 95% for similarity and 90% for overlapping.
The specialized information included in UTR entries is generated by using two programs: (i) UTRnote including information about the location of experimentally defined patterns collected in UTRsite and (ii) UTRrepeat (which uses RepeatMasker) including repetitive elements present in the Repbase database (19). The UTRsite entries describe the various regulatory elements present in UTRs whose functional role has been established on an experimental basis. Each UTRsite entry is constructed on the basis of information reported in the literature and revised by distinguished scientists experimentally working on the functional characterization of the relevant UTR regulatory element.
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CONTENT OF UTRdb |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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Table 1 reports a summary description of UTRdb (release 15.0) which in total contains 247 548 entries and 64 060 991 nt. On average >35% of entries resulted to be redundant and were then removed from the database. Vector contamination was found in 188 and 196 entries of 5'- and 3'-UTRs, respectively.
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5'-UTR sequences were defined as the mRNA region spanning from the cap site to the starting codon (excluded), whereas 3'-UTR sequences were defined as the mRNA region spanning from the stop codon (excluded) to the poly(A) starting site.
A sample entry of UTRdb is shown in Figure 1. The UTRdb entries have been formatted according to the EMBL database format.
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Table 2 reports functional patterns and repetitive elements included in UTRsite. More entries will be included in further releases. A sample UTRsite entry is reported in Figure 2. Functional patterns, defined on the basis of the information reported in the literature and/or advice by the scientists expert in the field, were described by using the pattern description syntax used in PatSearch program (22).
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AVAILABILITY OF UTRdb |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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UTRdb and UTRsite are publicly available by anonymous FTP (ftp://area.ba.cnr.it/pub/embnet/database/utr/). All internet resources we implemented for retrieval and functional analysis of 5'- and 3'-UTR sequences are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/. These include SRS retrieval (23) of UTRdb and UTRsite, also available at the EBI World Wide Web server (http://srs.ebi.ac.uk:80/), UTRscan and UTRblast. The UTRscan utility allows the enquirer to search user submitted sequences for any of the patterns collected in UTRsite. The UTRblast utility allows database searches against fully annotated UTRdb entries.
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CONCLUSIONS AND PERSPECTIVES |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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The important role that UTRs of eukaryotic mRNAs may play in gene regulation and expression is now widely recognized. Indeed, experimental studies have demonstrated that sequence motifs located in the UTRs are involved in crucial biological functions.
The huge amount of functionally equivalent sequences stored in UTRdb now makes possible the study of their structural and compositional features and the application of statistical methods for the identification of significant signals. Previous cleaning-up of databases is however necessary to avoid artefacts caused by redundant sequences. Even if statistical significance does not necessarily mean biological significance, it may provide useful indication for further experimental work, such as site-directed mutagenesis.
UTRdb will be updated with the new EMBL database releases and UTRsite will be continuously updated by adding new entries describing functional patterns whose biological role has been experimentally demonstrated.
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ACKNOWLEDGEMENTS |
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For revision of UTRsite entries we would like to thank Jim Malter (APP 3'-UTR stability control element), Alain Krol (SECIS), Matthias Hentze (IRE, 15-LOX DICE and msl-2), Bill Marzluff (histone stem–loop structure), Ann-Bin Shyu (ARE), Arturo Verrotti (CPE), Elizabeth Goodwin (TGE), Roger Kaspar (ribosomal protein mRNA TOP), Danuta Radzioch (TNF mRNA translation repression element), Ruben Boado (GLUT1 mRNA stabilizing element), Zendra E. Zehner (Vimentin 3'-UTR mRNA element), Shu-Yun Le (IRES), Anne Ephrussi (BRE), Howy Jacobs (rpmS12), Allen Miller (BYDV), John Parsch (adh DRE). This work was supported by Ministero dell’Istruzione e Ricerca, Italy [projects: Bioinformatics and Genomic Research (COFIN99), Programma ‘Biotecnologie’ (legge 95/95 – 5%), Programma ‘Studio di geni di interesse biomedico e agroalimentare’ (CEGBA)].
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FOOTNOTES |
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* To whom correspondence should be addressed. Tel: +39 02 58354915; Fax +39 02 58354912; Email: graziano.pesole{at}unimi.it
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REFERENCES |
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TOPABSTRACTINTRODUCTIONUTRdb GENERATIONCONTENT OF UTRdbAVAILABILITY OF UTRdbCONCLUSIONS AND PERSPECTIVESREFERENCES |
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R. Jarving, I. Jarving, R. Kurg, A. R. Brash, and N. Samel On the Evolutionary Origin of Cyclooxygenase (COX) Isozymes: CHARACTERIZATION OF MARINE INVERTEBRATE COX GENES POINTS TO INDEPENDENT DUPLICATION EVENTS IN VERTEBRATE AND INVERTEBRATE LINEAGES J. Biol. Chem., April 2, 2004; 279(14): 13624 - 13633. [Abstract] [Full Text] [PDF]
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T. Ruggiero, M. Olivero, A. Follenzi, L. Naldini, R. Calogero, and M. F. Di Renzo Deletion in a (T)8 microsatellite abrogates expression regulation by 3'-UTR Nucleic Acids Res., November 15, 2003; 31(22): 6561 - 6569. [Abstract] [Full Text] [PDF]
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S. Park-Lee, S. Kim, and I. A. Laird-Offringa Characterization of the Interaction between Neuronal RNA-binding Protein HuD and AU-rich RNA J. Biol. Chem., October 10, 2003; 278(41): 39801 - 39808. [Abstract] [Full Text] [PDF]
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S. A. Shabalina, A. Y. Ogurtsov, D. J. Lipman, and A. S. Kondrashov Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs Nucleic Acids Res., September 15, 2003; 31(18): 5433 - 5439. [Abstract] [Full Text] [PDF]
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F. Mignone, G. Grillo, S. Liuni, and G. Pesole Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis Nucleic Acids Res., August 1, 2003; 31(15): 4639 - 4645. [Abstract] [Full Text] [PDF]
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G. Grillo, F. Licciulli, S. Liuni, E. Sbisa, and G. Pesole PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences Nucleic Acids Res., July 1, 2003; 31(13): 3608 - 3612. [Abstract] [Full Text] [PDF]
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 W. Zhu, S. D. Schlueter, and V. Brendel Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping Plant Physiology, June 1, 2003; 132(2): 469 - 484. [Abstract] [Full Text] [PDF]
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D. De Pietri Tonelli, M. Mihailovich, R. Schnurbus, G. Pesole, F. Grohovaz, and D. Zacchetti Translational control of Scamper expression via a cell-specific internal ribosome entry site Nucleic Acids Res., May 15, 2003; 31(10): 2508 - 2513. [Abstract] [Full Text] [PDF]
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M. Olivero, T. Ruggiero, N. Coltella, A. Maffe', R. Calogero, E. Medico, and M. F. Di Renzo Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer Nucleic Acids Res., April 1, 2003; 31(7): e33 - e33. [Abstract] [Full Text] [PDF]
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 P. Sampath, B. Mazumder, V. Seshadri, and P. L. Fox Transcript-Selective Translational Silencing by Gamma Interferon Is Directed by a Novel Structural Element in the Ceruloplasmin mRNA 3' Untranslated Region Mol. Cell. Biol., March 1, 2003; 23(5): 1509 - 1519. [Abstract] [Full Text] [PDF]
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A. Romani, E. Guerra, M. Trerotola, and S. Alberti Detection and analysis of spliced chimeric mRNAs in sequence databanks Nucleic Acids Res., February 15, 2003; 31(4): e17 - e17. [Abstract] [Full Text] [PDF]
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I. Bar, F. Tissir, C. Lambert de Rouvroit, O. De Backer, and A. M. Goffinet The Gene Encoding Disabled-1 (DAB1), the Intracellular Adaptor of the Reelin Pathway, Reveals Unusual Complexity in Human and Mouse J. Biol. Chem., February 14, 2003; 278(8): 5802 - 5812. [Abstract] [Full Text] [PDF]
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I. Liebich, J. Bode, I. Reuter, and E. Wingender Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs) Nucleic Acids Res., August 1, 2002; 30(15): 3433 - 3442. [Abstract] [Full Text] [PDF]
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