John F Atkins

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. pmc A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment
    John F Atkins
    Biosciences Institute, University College, Cork, Ireland
    Microbiol Mol Biol Rev 73:178-210. 2009
  2. pmc Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression
    Pavel V Baranov
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
    Genome Biol 6:R25. 2005
  3. pmc Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs
    Michael Bekaert
    School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
    BMC Bioinformatics 9:178. 2008
  4. pmc Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virology 399:153-66. 2010
  5. pmc Recode-2: new design, new search tools, and many more genes
    Michael Bekaert
    School of Biology and Environmental Science, University College Dublin, Biosciences Institute, University College Cork, Ireland
    Nucleic Acids Res 38:D69-74. 2010
  6. pmc Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:193. 2009
  7. pmc Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome
    Gary Loughran
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 108:E1111-9. 2011
  8. pmc 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
  9. pmc A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment
    Virag Sharma
    Department of Biochemistry, University College Cork, Cork, Ireland
    Mol Biol Evol 28:3195-211. 2011
  10. doi request reprint Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Arch Virol 153:1379-83. 2008

Detail Information

Publications28

  1. pmc A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment
    John 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...
  2. pmc Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression
    Pavel 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...
  3. pmc Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs
    Michael 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...
  4. pmc Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virology 399:153-66. 2010
    ....
  5. pmc Recode-2: new design, new search tools, and many more genes
    Michael 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...
  6. pmc Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses
    Andrew 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...
  7. pmc Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome
    Gary 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...
  8. pmc 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...
  9. pmc A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment
    Virag 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...
  10. doi request reprint Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene
    Andrew 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...
  11. pmc Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 6:32. 2009
    ..Possible translation mechanisms for this unusually positioned ORF are discussed...
  12. pmc Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene
    Andrew 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...
  13. pmc Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences
    Ivaylo 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...
  14. pmc A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product
    Andrew 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'...
  15. doi request reprint Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function
    Ivaylo P Ivanov
    Biosciences Institute, University College Cork, Ireland
    J Mol Evol 70:289-302. 2010
    ....
  16. pmc A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation
    Ivaylo 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...
  17. pmc rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
    Patrick B F O'Connor
    Department of Biochemistry, University College Cork, Cork, Ireland
    Bioinformatics 29:1488-91. 2013
    ..Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints...
  18. pmc Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5
    Gary 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...
  19. pmc Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning
    Andrew E Firth
    Biosciences Institute, University College Cork, Cork, Ireland
    Virol J 7:17. 2010
    ..In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community...
  20. doi request reprint Frameshifting in alphaviruses: a diversity of 3' stimulatory structures
    Betty 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...
  21. pmc 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...
  22. pmc A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting
    Andrew 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'...
  23. pmc Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma
    Andrew 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...
  24. pmc uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs
    Ivaylo 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...
  25. ncbi request reprint ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
    Michael Bekaert
    Biosciences Institute, University College Cork, Cork, Ireland
    Bioinformatics 22:2463-5. 2006
    ..Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly...
  26. pmc Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene
    Andrew 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...
  27. pmc Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation
    Ivaylo 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...
  28. ncbi request reprint Recoding in bacteriophages and bacterial IS elements
    Pavel 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...