KnotInFrame: prediction of –1 ribosomal frameshift events

Theis C, Reeder J, Giegerich R (2008)
Nucleic Acids Research 36(18): 6013-6020.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA
DOI
URN
urn:nbn:de:0070-pub-17833575
Autor*in
Theis, Corinna; Reeder, Jens; Giegerich, RobertUniBi
Einrichtung
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > AG Praktische Informatik
Centrum für Biotechnologie > Arbeitsgruppe R. Giegerich
Abstract / Bemerkung
Programmed –1 ribosomal frameshift (–1 PRF) allows for alternative reading frames within one mRNA. First found in several viruses, it is now believed to exist in all kingdoms of life. Strong stimulators for –1 PRF are a heptameric slippery site and an RNA pseudoknot. Here, we present a new algorithm KnotInFrame, for the automatic detection of –1 PRF signals from genomic sequences. It finds the frameshifting stimulators by means of a specialized RNA-pseudoknot folding program, fast enough for genome-wide analyses. Evaluations on known –1 PRF signals demonstrate a high sensitivity.
Erscheinungsjahr
2008
Zeitschriftentitel
Nucleic Acids Research
Band
36
Ausgabe
18
Seite(n)
6013-6020
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1783357

Zitieren

Theis C, Reeder J, Giegerich R. KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research. 2008;36(18):6013-6020.
Theis, C., Reeder, J., & Giegerich, R. (2008). KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research, 36(18), 6013-6020. https://doi.org/10.1093/nar/gkn578
Theis, Corinna, Reeder, Jens, and Giegerich, Robert. 2008. “KnotInFrame: prediction of –1 ribosomal frameshift events”. Nucleic Acids Research 36 (18): 6013-6020.
Theis, C., Reeder, J., and Giegerich, R. (2008). KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research 36, 6013-6020.
Theis, C., Reeder, J., & Giegerich, R., 2008. KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research, 36(18), p 6013-6020.
C. Theis, J. Reeder, and R. Giegerich, “KnotInFrame: prediction of –1 ribosomal frameshift events”, Nucleic Acids Research, vol. 36, 2008, pp. 6013-6020.
Theis, C., Reeder, J., Giegerich, R.: KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research. 36, 6013-6020 (2008).
Theis, Corinna, Reeder, Jens, and Giegerich, Robert. “KnotInFrame: prediction of –1 ribosomal frameshift events”. Nucleic Acids Research 36.18 (2008): 6013-6020.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T08:48:51Z
MD5 Prüfsumme
c229441d9399b2ac75ba28995b398df5


29 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy.
Laumont CM, Perreault C., Cell Mol Life Sci 75(4), 2018
PMID: 28823056
Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene.
Meydan S, Klepacki D, Karthikeyan S, Margus T, Thomas P, Jones JE, Khan Y, Briggs J, Dinman JD, Vázquez-Laslop N, Mankin AS., Mol Cell 65(2), 2017
PMID: 28107647
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.
Lim CS, Brown CM., Front Microbiol 8(), 2017
PMID: 29354101
Virus surveys of Capsicum spp. in the Republic of Benin reveal the prevalence of pepper vein yellows virus and the identification of a previously uncharacterised polerovirus species.
Afouda L, Kone D, Zinsou V, Dossou L, Kenyon L, Winter S, Knierim D., Arch Virol 162(6), 2017
PMID: 28220324
Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso.
Palanga E, Martin DP, Galzi S, Zabré J, Bouda Z, Neya JB, Sawadogo M, Traore O, Peterschmitt M, Roumagnac P, Filloux D., Arch Virol 162(7), 2017
PMID: 28337544
Molecular detection of a novel totivirus from golden shiner (Notemigonus crysoleucas) baitfish in the USA.
Mor SK, Phelps NB., Arch Virol 161(8), 2016
PMID: 27231008
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.
Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV., Nucleic Acids Res 44(15), 2016
PMID: 27436286
The RNA shapes studio.
Janssen S, Giegerich R., Bioinformatics 31(3), 2015
PMID: 25273103
Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting.
Caliskan N, Peske F, Rodnina MV., Trends Biochem Sci 40(5), 2015
PMID: 25850333
Characterization of the Complete Genome of a Novel Polerovirus Infecting Sauropus androgynus in Thailand
Knierim D, Maiss E, Menzel W, Winter S, Kenyon L., Journal of phytopathology. 163(9), 2015
PMID: IND603502138
An infectious RNA with a hepta-adenosine stretch responsible for programmed -1 ribosomal frameshift derived from a full-length cDNA clone of Hibiscus latent Singapore virus.
Niu S, Cao S, Wong SM., Virology 449(), 2014
PMID: 24418557
A high-definition view of functional genetic variation from natural yeast genomes.
Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G., Mol Biol Evol 31(4), 2014
PMID: 24425782
Molecular characterization and phylogenetic analysis of the genome of porcine torovirus.
Sun H, Lan D, Lu L, Chen M, Wang C, Hua X., Arch Virol 159(4), 2014
PMID: 24122107
Genetic diversification of penaeid shrimp infectious myonecrosis virus between Indonesia and Brazil.
Naim S, Brown JK, Nibert ML., Virus Res 189(), 2014
PMID: 24874195
Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.
Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O., Nucleic Acids Res 42(11), 2014
PMID: 24875478
Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription.
Huang Q, Purzycka KJ, Lusvarghi S, Li D, Legrice SF, Boeke JD., RNA 19(3), 2013
PMID: 23329695
Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication.
Nakano K, Ando T, Yamagishi M, Yokoyama K, Ishida T, Ohsugi T, Tanaka Y, Brighty DW, Watanabe T., Microbes Infect 15(6-7), 2013
PMID: 23541980
Ligand-inducible formation of RNA pseudoknot.
Matsumoto S, Hong C, Otabe T, Murata A, Nakatani K., Bioorg Med Chem Lett 23(12), 2013
PMID: 23664873
Identification of the nature of reading frame transitions observed in prokaryotic genomes.
Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M., Nucleic Acids Res 41(13), 2013
PMID: 23649834
HTLV-1 Rex: the courier of viral messages making use of the host vehicle.
Nakano K, Watanabe T., Front Microbiol 3(), 2012
PMID: 22973269
On programmed ribosomal frameshifting: the alternative proteomes.
Ketteler R., Front Genet 3(), 2012
PMID: 23181069
Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast.
Belew AT, Advani VM, Dinman JD., Nucleic Acids Res 39(7), 2011
PMID: 21109528
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1.
Lu ZH, di Domenico A, Wright SH, Knight PA, Whitelaw CB, Pemberton AD., BMC Genomics 12(), 2011
PMID: 21324158
Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.
Ahmed F, Benedito VA, Zhao PX., Front Plant Sci 2(), 2011
PMID: 22639614
Recode-2: new design, new search tools, and many more genes.
Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV., Nucleic Acids Res 38(database issue), 2010
PMID: 19783826
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.
Sperschneider J, Datta A., Nucleic Acids Res 38(7), 2010
PMID: 20123730
Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm.
Antonov I, Borodovsky M., J Bioinform Comput Biol 8(3), 2010
PMID: 20556861
Parallel germline infiltration of a lentivirus in two Malagasy lemurs.
Gilbert C, Maxfield DG, Goodman SM, Feschotte C., PLoS Genet 5(3), 2009
PMID: 19300488
Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron.
Zhang L, Bao P, Leibowitz MJ, Zhang Y., RNA 15(11), 2009
PMID: 19710184

30 References

Daten bereitgestellt von Europe PubMed Central.

Genetic Control of Biochemical Reactions in Neurospora.
Beadle GW, Tatum EL., Proc. Natl. Acad. Sci. U.S.A. 27(11), 1941
PMID: 16588492
Trans-splicing of nematode premessenger RNA
Nilsen TW., 1993
Coupling of open reading frames by translational bypassing.
Herr AJ, Atkins JF, Gesteland RF., Annu. Rev. Biochem. 69(), 2000
PMID: 10966462
A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs.
Walczak R, Westhof E, Carbon P, Krol A., RNA 2(4), 1996
PMID: 8634917
Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae.
Jacobs JL, Belew AT, Rakauskaite R, Dinman JD., Nucleic Acids Res. 35(1), 2006
PMID: 17158156
Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency.
Kontos H, Napthine S, Brierley I., Mol. Cell. Biol. 21(24), 2001
PMID: 11713298
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.
Namy O, Moran SJ, Stuart DI, Gilbert RJ, Brierley I., Nature 441(7090), 2006
PMID: 16688178
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
Leger M, Dulude D, Steinberg SV, Brakier-Gingras L., Nucleic Acids Res. 35(16), 2007
PMID: 17704133
Identification of putative programmed -1 ribosomal frameshift signals in large DNA databases.
Hammell AB, Taylor RC, Peltz SW, Dinman JD., Genome Res. 9(5), 1999
PMID: 10330121
Predicting genes expressed via -1 and +1 frameshifts.
Moon S, Byun Y, Kim HJ, Jeong S, Han K., Nucleic Acids Res. 32(16), 2004
PMID: 15371551
Towards a computational model for -1 eukaryotic frameshifting sites.
Bekaert M, Bidou L, Denise A, Duchateau-Nguyen G, Forest JP, Froidevaux C, Hatin I, Rousset JP, Termier M., Bioinformatics 19(3), 2003
PMID: 12584117
RNAMotif, an RNA secondary structure definition and search algorithm.
Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R., Nucleic Acids Res. 29(22), 2001
PMID: 11713323
A dynamic programming algorithm for RNA structure prediction including pseudoknots.
Rivas E, Eddy SR., J. Mol. Biol. 285(5), 1999
PMID: 9925784
RECODE 2003.
Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, Atkins JF., Nucleic Acids Res. 31(1), 2003
PMID: 12519954
A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal.
Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD., PLoS Biol. 3(6), 2005
PMID: 15884978
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
PMID: 6163133
Fast folding and comparison of RNA secondary structures
Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, Schuster P., 1994
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
Reeder J, Giegerich R., 2004
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.
Reeder J, Steffen P, Giegerich R., Nucleic Acids Res. 35(Web Server issue), 2007
PMID: 17478505
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
A discipline of dynamic programming over sequence data
Giegerich R, Meyer C, Steffen P., 2004
Versatile and declarative dynamic programming using pair algebras
Steffen P, Giegerich R., 2005
Challenges in the compilation of a domain specific language for dynamic programming.
Giegerich R, Steffen P., 2006
Compiling a domain specific language for dynamic programming.
Steffen P., 2006
Characterization of the frameshift signal of Edr, a mammalian example of programmed -1 ribosomal frameshifting.
Manktelow E, Shigemoto K, Brierley I., Nucleic Acids Res. 33(5), 2005
PMID: 15767280
PseudoBase: structural information on RNA pseudoknots.
van Batenburg FH, Gultyaev AP, Pleij CW., Nucleic Acids Res. 29(1), 2001
PMID: 11125088
Thermodynamic matchers: strengthening the significance of RNA folding energies
Höchsmann T, Höchsmann M, Giegerich R., 2006
PRFdb: a database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals.
Belew AT, Hepler NL, Jacobs JL, Dinman JD., BMC Genomics 9(), 2008
PMID: 18637175
A partition function algorithm for nucleic acid secondary structure including pseudoknots.
Dirks RM, Pierce NA., J Comput Chem 24(13), 2003
PMID: 12926009
Locomotif: from graphical motif description to RNA motif search.
Reeder J, Reeder J, Giegerich R., Bioinformatics 23(13), 2007
PMID: 17646322
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 18820303
PubMed | Europe PMC

Suchen in

Google Scholar