Research Topics
Genomes and Genes | John F AtkinsSummaryAffiliation: University of Utah Country: USA Publications
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Publications
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignmentJohn F Atkins
Biosciences Institute, University College, Cork, Ireland
Microbiol Mol Biol Rev 73:178-210. 2009..Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized...- Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expressionPavel V Baranov
Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
Genome Biol 6:R25. 2005..This probably leads to selection against most slippage-prone sequences in coding regions... - Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAsMichael Bekaert
School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
BMC Bioinformatics 9:178. 2008..This manuscript describes a rapid and accurate computer tool for antizyme CDS detection that requires minimal human involvement... - Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flavivirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virology 399:153-66. 2010.... - Recode-2: new design, new search tools, and many more genesMichael Bekaert
School of Biology and Environmental Science, University College Dublin, Biosciences Institute, University College Cork, Ireland
Nucleic Acids Res 38:D69-74. 2010..Recode-2 is available at http://recode.ucc.ie... - Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistrovirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:193. 2009..We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop... - Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genomeGary Loughran
Biosciences Institute, University College Cork, Cork, Ireland
Proc Natl Acad Sci U S A 108:E1111-9. 2011..Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses... - Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)Pavel V Baranov
Biochemistry Department, University College Cork, Cork, Ireland
RNA Biol 8:637-47. 2011..Three other proposed PRF candidates (Xbp1, CG32736, CG14047) with switches in conservation of reading frames are likely explained by mechanisms other than PRF... - A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignmentVirag Sharma
Department of Biochemistry, University College Cork, Cork, Ireland
Mol Biol Evol 28:3195-211. 2011..In addition to the identification of a large number of recoded genes, a surprising observation is that nearly half of them are expressed via PTR-a mechanism that, in contrast to PRF, has not yet received substantial attention... - Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:222. 2009..We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein... 
Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Arch Virol 153:1379-83. 2008..The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis...- Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijivirusesAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:32. 2009..Possible translation mechanisms for this unusually positioned ORF are discussed... - Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory functionIvaylo P Ivanov
Biosciences Institute, University College Cork, Ireland
J Mol Evol 70:289-302. 2010.... - A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa productAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:136. 2009..We propose that the new ORF utilizes a non-AUG initiation codon--namely a conserved CUG codon in a strong Kozak context--upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'... - Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequencesIvaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland
Nucleic Acids Res 39:4220-34. 2011..In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data... - A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulationIvaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
Nucleic Acids Res 38:353-9. 2010..The uORF-mediated polyamine responsive autoregulatory circuits found in polyamine pathway mRNAs exemplify the translationally regulated dynamic interface between components of the proteome and metabolism... - Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5Gary Loughran
Biosciences Institute, University College Cork, Ireland
Nucleic Acids Res 40:2898-906. 2012..The results obtained provide the basis for a model in which auto- and cross-regulation of eIF5 and eIF1 translation establish a regulatory feedback loop that would stabilize the stringency of start codon selection... - Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanningAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 7:17. 2010..RESULTS: Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively)... - Frameshifting in alphaviruses: a diversity of 3' stimulatory structuresBetty Y W Chung
Biosciences Institute, University College Cork, Cork, Ireland
J Mol Biol 397:448-56. 2010..The analysis, both experimental and bioinformatic, significantly expands the known repertoire of -1 frameshifting stimulators in mammalian and insect systems... - Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)Ivaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland
Proc Natl Acad Sci U S A 107:18056-60. 2010..The capacity for the cellular level of eIF1 to impact initiation through the variable stringency of initiation codon selection likely has significant consequences for the proteome in eukaryotes... - A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshiftingAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 6:14. 2009..We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'... - Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigmaAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 5:108. 2008..In protein gels, 6K migrates as a doublet--a result that, to date, has been attributed to differing degrees of acylation. Nonetheless, despite many years of research, its role is still relatively poorly understood... - uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologsIvaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland
Proc Natl Acad Sci U S A 105:10079-84. 2008..This repression is part of an autoregulatory circuit, and one of its sensors is the AUU codon, which suggests that translation initiation codon identity is likely used for regulation in eukaryotes... - Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping geneAndrew E Firth
Biosciences Institute, University College Cork, Cork, Ireland
Virol J 5:62. 2008..The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5-10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels... 
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshiftingMichael Bekaert
Biosciences Institute, University College Cork, Cork, Ireland
Bioinformatics 22:2463-5. 2006..AVAILABILITY: The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa..- Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservationIvaylo P Ivanov
Biosciences Institute, University College Cork, Cork, Ireland
Nucleic Acids Res 35:1842-58. 2007..Among these are RNA pseudoknots, RNA stem-loops, conserved primary RNA sequences, nascent peptide sequences and branch-specific 'shifty' codons... - Recoding in bacteriophages and bacterial IS elementsPavel V Baranov
Bioscience Institute, University College Cork, Cork, Ireland
Trends Genet 22:174-81. 2006..Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture...