Genomes and Genes
ribonucleic acid regulatory sequences
Summary: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
- Liu J, Wang J, Hu J, Tian B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics. 2005;6:89 pubmed..This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large. ..
- Stamm S, Riethoven J, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, et al. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res. 2006;34:D46-55 pubmed..ASD data has been integrated with Ensembl genome annotation project as a Distributed Annotation System (DAS) resource and can be viewed on Ensembl genome browser. The ASD resource is presented at (http://www.ebi.ac.uk/asd). ..
- Zhu H, Hinman M, Hasman R, Mehta P, Lou H. Regulation of neuron-specific alternative splicing of neurofibromatosis type 1 pre-mRNA. Mol Cell Biol. 2008;28:1240-51 pubmed..In addition to providing the first mechanistic insight into tissue-specific control of NF1 splicing, these studies establish a novel strategy whereby Hu proteins regulate RNA processing. ..
- Hirose T, Sugiura M. Multiple elements required for translation of plastid atpB mRNA lacking the Shine-Dalgarno sequence. Nucleic Acids Res. 2004;32:3503-10 pubmed..We hypothesize for translational initiation of the atpB mRNA that the ribosome enters an upstream region, slides to the start codon and forms an initiation complex with p50 and other components. ..
- Bengert P, Dandekar T. Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res. 2004;32:W154-9 pubmed..The program has been implemented and is available both as local software for in-house installation and as a web server at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/Riboswitch/. ..
- Holste D, Huo G, Tung V, Burge C. HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res. 2006;34:D56-62 pubmed..A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu. ..
- Barreau C, Paillard L, Osborne H. AU-rich elements and associated factors: are there unifying principles?. Nucleic Acids Res. 2005;33:7138-50 pubmed..The potential relationship between mRNA stability and translation is also discussed. Finally, we present several hypotheses that could unify the published data and suggest avenues for future research. ..
- Raineri I, Wegmueller D, Gross B, Certa U, Moroni C. Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference. Nucleic Acids Res. 2004;32:1279-88 pubmed
- Rodionov D, Vitreschak A, Mironov A, Gelfand M. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?. Nucleic Acids Res. 2003;31:6748-57 pubmed..Finally, the most likely candidates for genes of lysine biosynthesis missing in Gram- positive bacteria were identified using the genome context analysis. ..
- Bengert P, Dandekar T. A software tool-box for analysis of regulatory RNA elements. Nucleic Acids Res. 2003;31:3441-5 pubmed..The tool box has been implemented as a WWW server at http://wb2x01.biozentrum.uni-wuerzburg.de/. ..
- Holcik M, Gordon B, Korneluk R. The internal ribosome entry site-mediated translation of antiapoptotic protein XIAP is modulated by the heterogeneous nuclear ribonucleoproteins C1 and C2. Mol Cell Biol. 2003;23:280-8 pubmed..Given the central role of XIAP in the regulation of apoptosis these results are important for our understanding of the control of apoptosis. ..
- Heise T, Sommer G, Reumann K, Meyer I, Will H, Schaal H. The hepatitis B virus PRE contains a splicing regulatory element. Nucleic Acids Res. 2006;34:353-63 pubmed..We discuss a model in which the regulation of pgRNA splicing depends on cellular factors interacting with the PRE. ..
- Gilbert S, Stoddard C, Wise S, Batey R. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol. 2006;359:754-68 pubmed
- Singh N, Singh R, Androphy E. Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes. Nucleic Acids Res. 2007;35:371-89 pubmed..Our findings reveal for the first time the critical role of RNA structure in regulation of alternative splicing of human SMN. ..
- An P, Grabowski P. Exon silencing by UAGG motifs in response to neuronal excitation. PLoS Biol. 2007;5:e36 pubmed..These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation. ..
- Mercado P, Ayala Y, Romano M, Buratti E, Baralle F. Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene. Nucleic Acids Res. 2005;33:6000-10 pubmed..Altogether, our results suggest that exonic and intronic enhancers have evolved to balance the negative effects of the two silencers located in intron 2 and hence rescue the constitutive exon 3 inclusion in apoA-II mRNA. ..
- Pfingsten J, Costantino D, Kieft J. Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science. 2006;314:1450-4 pubmed..Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA. ..
- Li Y, Bor Y, Misawa Y, Xue Y, Rekosh D, Hammarskjold M. An intron with a constitutive transport element is retained in a Tap messenger RNA. Nature. 2006;443:234-7 pubmed..Thus, CTEs are likely to be important elements that facilitate efficient expression of mammalian mRNAs with retained introns. ..
- Abreu Goodger C, Merino E. RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res. 2005;33:W690-2 pubmed..Alternatively, the genome context of all other genes regulated by the same element can be explored with our genome context tool (GeConT). RibEx is available at http://www.ibt.unam.mx/biocomputo/ribex.html. ..
- Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309:1559-63 pubmed..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. ..
- Ottink O, Rampersad S, Tessari M, Zaman G, Heus H, Wijmenga S. Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism. RNA. 2007;13:2202-12 pubmed
- Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey P, et al. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2005;33:D141-6 pubmed..g. GO term, PFAM domain, etc.). All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://www.ba.itb.cnr.it/UTR/. ..
- Zhang X, Chasin L. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 2004;18:1241-50 pubmed..The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA. ..
- Plant E, Wang P, Jacobs J, Dinman J. A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. Nucleic Acids Res. 2004;32:784-90 pubmed..Analysis of the mRNA decay profiles of the frameshift-signal- containing reporter mRNAs also supports the notion that NMD remains active on mRNAs beyond the 'pioneer round' of translation in yeast. ..
- Thanaraj T, Stamm S, Clark F, Riethoven J, Le Texier V, Muilu J. ASD: the Alternative Splicing Database. Nucleic Acids Res. 2004;32:D64-9 pubmed..The data are presented on our ASD web pages (http://www.ebi.ac.uk/asd). ..
- Bonnal S, Boutonnet C, Prado Lourenco L, Vagner S. IRESdb: the Internal Ribosome Entry Site database. Nucleic Acids Res. 2003;31:427-8 pubmed..This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/. ..
- Toledo Arana A, Dussurget O, Nikitas G, Sesto N, Guet Revillet H, Balestrino D, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature. 2009;459:950-6 pubmed publisher..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria. ..
- Romero López C, Berzal Herranz A. A long-range RNA-RNA interaction between the 5' and 3' ends of the HCV genome. RNA. 2009;15:1740-52 pubmed publisher..The 5'-3' end bridge may have a role in viral translation modulation and in the switch from protein synthesis to RNA replication. ..
- Yeo G, Van Nostrand E, Nostrand E, Liang T. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet. 2007;3:e85 pubmed..Our results demonstrate that ISREs are crucial building blocks in understanding general and tissue-specific AS regulation and the biological pathways and functions regulated by these AS events. ..
- Zhang H, Lee J, Tian B. Biased alternative polyadenylation in human tissues. Genome Biol. 2005;6:R100 pubmed
- Noeske J, Buck J, Fürtig B, Nasiri H, Schwalbe H, Wöhnert J. Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res. 2007;35:572-83 pubmed..The tertiary interaction motif is stable outside the riboswitch context. ..
- Gilbert S, Love C, Edwards A, Batey R. Mutational analysis of the purine riboswitch aptamer domain. Biochemistry. 2007;46:13297-309 pubmed
- ..Although modern riboswitches might be the last holdouts of primitive genetic elements, some are capable of sensory and regulatory feats that are competitive with their protein counterparts. ..
- Pacheco A, López de Quinto S, Ramajo J, Fernandez N, Martinez Salas E. A novel role for Gemin5 in mRNA translation. Nucleic Acids Res. 2009;37:582-90 pubmed publisher..Thus, beyond its role in snRNPs biogenesis, Gemin5 also functions as a modulator of translation activity. ..
- Gilbert S, Mediatore S, Batey R. Modified pyrimidines specifically bind the purine riboswitch. J Am Chem Soc. 2006;128:14214-5 pubmed..Using isothermal titration calorimetry and X-ray crystallography, the binding of these compounds is characterized. ..
- Lei H, Day I, Vorechovsky I. Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer. Nucleic Acids Res. 2005;33:3897-906 pubmed
- Winkler W, Nahvi A, Breaker R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 2002;419:952-6 pubmed..This metabolite-sensing regulatory system provides an example of a 'riboswitch' whose evolutionary origin might pre-date the emergence of proteins. ..
- Wagner E, Garcia Blanco M. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol Cell. 2002;10:943-9 pubmed..Depletion of endogenous PTB using RNAi increases exon IIIb inclusion in transcripts derived from minigenes and from the endogenous FGF-R2 gene. These data demonstrate that PTB is a negative regulator of exon definition in vivo. ..
- Nahvi A, Barrick J, Breaker R. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 2004;32:143-50 pubmed
- Rodionov D, Vitreschak A, Mironov A, Gelfand M. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 2004;32:3340-53 pubmed..In particular, Oceanobacillus iheyensis possibly uses a homolog of the betaine-homocysteine methyltransferase bhmT gene from vertebrates to substitute missing bacterial-type methionine synthases. ..
- Fu X. Towards a splicing code. Cell. 2004;119:736-8 pubmed
- Hall Pogar T, Zhang H, Tian B, Lutz C. Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res. 2005;33:2565-79 pubmed..5-fold. Our data suggest for the first time that alternative polyadenylation of COX-2 is an important post-transcriptional regulatory event. ..
- Sasaki T, Yukawa Y, Wakasugi T, Yamada K, Sugiura M. A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts. Plant J. 2006;47:802-10 pubmed..These results suggest that distinct editing mechanisms are present in chloroplasts. ..
- Wang J, Smith P, Krainer A, Zhang M. Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res. 2005;33:5053-62 pubmed..Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing. ..
- Hundsdoerfer P, Thoma C, Hentze M. Eukaryotic translation initiation factor 4GI and p97 promote cellular internal ribosome entry sequence-driven translation. Proc Natl Acad Sci U S A. 2005;102:13421-6 pubmed
- Blaxall B, Pende A, Wu S, Port J. Correlation between intrinsic mRNA stability and the affinity of AUF1 (hnRNP D) and HuR for A+U-rich mRNAs. Mol Cell Biochem. 2002;232:1-11 pubmed..Although the relative affinity ofAUF1 and HuR are generally predictive of mRNA stability, we find that certain mRNA sequences do not conform to these generalizations. ..
- Kostadinov R, Malhotra N, Viotti M, Shine R, D ANTONIO L, Bagga P. GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic Acids Res. 2006;34:D119-24 pubmed..GRSDB is a good resource for researchers interested in investigating the functional relevance of G-quadruplexes, especially in the context of alternative RNA processing. It can be accessed at http://bioinformatics.ramapo.edu/grsdb/. ..
- Batey R. Structures of regulatory elements in mRNAs. Curr Opin Struct Biol. 2006;16:299-306 pubmed..Another highly structured mRNA element, the viral internal ribosomal entry site, is able to manipulate the ribosome and replace the function of initiation factors to promote gene expression. ..
- Huang H, Chien C, Jen K, Huang H. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006;34:W429-34 pubmed..An intuitive user interface is designed to facilitate the comprehensive annotation of user-submitted mRNA sequences. The RegRNA web server is now available at http://RegRNA.mbc.NCTU.edu.tw/. ..
- Gottesman S. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet. 2005;21:399-404 pubmed..Because these non-coding RNAs act post-transcriptionally, they impose a regulatory step that is independent of and epistatic to any transcriptional signals for their target mRNAs. ..
- Minovitsky S, Gee S, Schokrpur S, Dubchak I, Conboy J. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res. 2005;33:714-24 pubmed..We further speculate that highly conserved UGCAUG-binding protein(s) related to the recently described Fox-1 splicing factor play a critical role in mediating this specificity. ..
- Jacobs G, Stockwell P, Tate W, Brown C. Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res. 2006;34:D37-40 pubmed..Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at http://uther.otago.ac.nz/Transterm.html. ..
- Blount K, Breaker R. Riboswitches as antibacterial drug targets. Nat Biotechnol. 2006;24:1558-64 pubmed..Herein we will summarize the experiments validating riboswitches as drug targets, describe the existing technology for riboswitch drug discovery and discuss the challenges that may face riboswitch drug discoverers. ..