RegRNA
A Regulatory RNA Motifs and Elements Finder
  Release 1.0, Jan 2006
 
 
 

RegRNA: A Regulatory RNA Motifs and Elements Finder

We establish an integrated web server, namely RegRNA, to identify the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified. The regulatory RNA motifs supported in RegRNA are categorized into several classes:

  • Motifs in mRNA 5'-UTR and 3'-UTR.
  • Motifs involved in mRNA splicing.
  • Motifs involved in transcriptional regulation.
  • Other motifs in mRNA, such as riboswitches.
  • Prediction of the splice sites, such as splicing donor/acceptor sites.
  • RNA structural features, such as inverted repeat.
  • miRNA target sites.

Finally, the RegRNA web server designs a variety of interface to facilitate the analysis for the homologs of the regulatory RNA motifs.


Information Flow
 

    Figure 1 shows the information flow of RegRNA. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (a) motifs in mRNA 5' -UTR and 3' -UTR; (b) motifs involved in mRNA splicing; (c) motifs involved in transcriptional regulation; (d) riboswitches; (e) splicing donor/acceptor sites; (f) inverted repeat; and (g) miRNA target sites.

     This work collected known regulatory RNA motifs and elements via a literature survey and by integrating a variety of regulatory RNA motif databases such as UTRSite (1) , TRANSFAC (8) , ASD (9) , miRBase (10) , and miRNAMap (11) . The UTRSite (Release 16) stores a collection of regulatory RNA located in 5 ' -UTR and 3 ' - UTR, whose function and structure were experimentally determined (1) . Additionally, other translational regulatory elements found in 5' -UTR and 3' -UTR are also obtained via a literature survey. The TRANSFAC database ( Release 7.4 ) (8) collects known transcriptional factors, their binding sites, nucleotide distribution matrices and regulated genes. Those transcriptional regulatory sites located in pre-mRNA or mature mRNA sequences were extracted. Such sites can occur in 5' -UTR, introns or exons. Riboswitches are natural genetic control elements typically located in untranslated regions (UTRs) of mRNA sequence to form a binding pocket for a metabolite that regulates that gene expression. Other the riboswitch structural motifs were also extracted from literature survey.

    The alternative splicing database (ASD) is a literature-based data set containing sequences and properties of alternatively spliced exons, functional enumeration of observed splicing events, and characterization of splicing regulatory elements (9) . In addition to the well-known splice sites, such as donor sites and acceptor sites, the conserved sequences in exonic and intronic regions are reportedly involved in an alternative splicing mechanism. In addition to the splicing motifs from ASD, numerous exonic splicing enhancer (ESE) and exonic splicing silencers (ESS) were obtained from literatures. The miRBase database (Release 7.1) (10) provides comprehensive microRNA sequence data, annotation and predicted gene targets. The known miRNA genes in three mammalian genomes?human, mouse, and rat?were obtained from miRBase (10) .

     The RegRNA currently collects 1274 regulatory motifs (Table 1). For instance, there are 40 regulatory RNA motifs located in 5' -UTR and 3' -UTR. The number of motifs involved in splicing is 43. In total, 744 known miRNAs in humans, mice, and rats were obtained.

     As to the regulatory RNA motifs in the form of primary structures represented as consensus patterns or sequence patterns, RegRNA integrates several motif identification tools, such as EMBOSS-fuzznuc (12) , EMBOSS-einverted (12) , and GeneSplicer (13) to detect the homologs of the regulatory RNA motifs collected in RegRNA (Table 2).

    The fuzznuc of EMBOSS package is applied to search a consensus pattern against a sequence . The einverted of EMBOSS package is applied to detect inverted repeats in a nucleotide sequence. GeneSplicer (13) was developed for determining splice sites in eukaryotic mRNA by combining several schemes that have already proven successful in characterizing the patterns surrounding donor and acceptor sites. Moreover, for identifying miRNA targets, miRanda (14) is applied to detect the miRNA target sites in a sequence that complimentary hybridizes to the mature mi RNAs . The Minimum Free Energy (MFE) of the miRNA?target duplex is determined by miRanda when predicting the miRNA target sites.

    As to the regulatory RNA motifs in the form of secondary structures represented as RNA structural descriptors (7) , RegRNA integrates RNAMotif to identify the homologs of regulatory RNA structural motifs in user-submitted sequences (Table 2). Some of regulatory RNA motifs in 5' -UTR and 3' -UTR and riboswitches are represented as RNA structural descriptors in advance for searching the homologs against the user-submitted sequences.

    Upon submission to the website, the input sequence is then analyzed and the prediction results are presented via both textual interface and graphical interface. Users can differentiate clearly between different regulatory RNA motifs and link to detailed descriptions via hyperlinks. If the detected homologs are regulatory RNA structural motifs, the RNA secondary structure of the detected homologs are generated by mfold (15) and provided on the web.

 
Figure 1. The RegRNA information flow.

Statistics and Comparisons
 

Types of Regulatory RNA Motifs

Number of Entries

Data Sources

In mRNA 5'-UTR and 3'-UTR

40

UTRSite (1)

Riboswitches

14

Literature survey

Involved in splicing (exonic)

176

Literature survey, ASD (9)

Involved in splicing (intronic)

91

Literature survey, ASD (9)

Transcriptional regulation (exon)

21

Literature survey, TRANSFAC (8)

Transcriptional regulation (intron)

156

Literature survey, TRANSFAC (8)

Transcriptional regulation (UTR)

22

Literature survey, TRANSFAC (8)

miRNA (human, mouse, and rat)

744

miRBase (10)

Total

1274

 

Table 1. RegRNA statistics.
 

Supported Analyzing Functions

Characteristics of Regulatory Motifs

Types of Regulatory RNA Motifs

Integrated Tools

Consensus pattern search

Sequence
Pattern

Motifs involved in mRNA splicing and regulation of transcription

EMBOSS-fuzznuc (12)

Splicing sites

Sequence
Pattern

Prediction of the splice sites

GeneSplicer (13)

RNA structural elements

Secondary Structure

Inverted repeat

EMBOSS-einverted (12)

RNA structural motif search

Secondary Structure

Motifs in mRNA 5'-UTR, 3'-UTR and open reading frames

RNAMotif (7)
PatSearch (2)

miRNA target sites

Duplex of nucleotide

miRNA target sites

miRanda (14)

Table 2. RegRNA computational tools.
 

Comparing Tools

Database Support

RNA structural Motif search

Consensus Pattern Search

Splicing Sites

Inverted Repeat

miRNA Targets

User Interface

RNAMotif (7)

-

User-defined

Yes

-

-

-

-

PatSearch (2)

Yes

User-defined

Yes

-

-

-

Yes

RibEx (5)

Yes

Riboswitch

-

-

-

-

-

Riboswitch finder (4)

Yes

Riboswitch

-

-

-

-

Yes

UTRScan (6)

Yes

Motifs in 5fUTR and 3fUTR

Yes

-

-

-

Yes

Transterm (3)

Yes

Motifs in 5fUTR, 3fUTR and ORF

Yes

-

-

-

Yes

RegRNA

Yes

User-defined, Riboswitch, Motifs in 5fUTR, 3fUTR and ORF

Yes

Yes

Yes

Yes

Yes

Table 3. Comparison of RegRNA and other tools and websites.

References

 

Mignone, F., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Kersey, P.J., Duarte, J., Saccone, C. and Pesole, G. (2005) UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res , 33, D141-146.

Grillo, G., Licciulli, F., Liuni, S., Sbisa, E. and Pesole, G. (2003) PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res , 31, 3608-3612.

Jacobs, G.H., Stockwell, P.A., Tate, W.P. and Brown, C.M. (2006) Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res , 34, D37-40.

Bengert, P. and Dandekar, T. (2004) Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res , 32, W154-159.

Abreu-Goodger, C. and Merino, E. (2005) RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res , 33, W690-692.

Pesole, G. and Liuni, S. (1999) Internet resources for the functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. Trends Genet , 15, 378.

Macke, T.J., Ecker, D.J., Gutell, R.R., Gautheret, D., Case, D.A. and Sampath, R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res , 29, 4724-4735.

Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res , 34, D108-110.

Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L. and Thanaraj, T.A. (2006) ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res , 34, D46-55.

Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res , 34, D140-144.

Hsu, P.W., Huang, H.D., Hsu, S.D., Lin, L.Z., Tsou, A.P., Tseng, C.P., Stadler, P.F., Washietl, S. and Hofacker, I.L. (2006) miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res , 34, D135-139.

Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet , 16, 276-277.

Pertea, M., Lin, X. and Salzberg, S.L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res , 29, 1185-1190.

Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol , 5, R1.

Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res , 31, 3406-3415.


Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan
Contact with Dr. Hsien-Da Huang