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 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
  3. pmc Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL
    Olga L Gurvich
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
    Nucleic Acids Res 39:3079-92. 2011
  4. pmc Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element
    Andrew E Firth
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Nucleic Acids Res 39:6679-91. 2011
  5. 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
  6. 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
  7. pmc Maintenance of the correct open reading frame by the ribosome
    Thomas M Hansen
    Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112 5330, USA
    EMBO Rep 4:499-504. 2003
  8. 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
  9. pmc Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons
    Michael T Howard
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
    EMBO J 24:1596-607. 2005
  10. 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

Collaborators

Detail Information

Publications63

  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 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...
  3. pmc Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL
    Olga L Gurvich
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
    Nucleic Acids Res 39:3079-92. 2011
    ..This finding of incidental, rather than utilized, frameshifting is cautionary for other studies of programmed frameshifting...
  4. pmc Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element
    Andrew E Firth
    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Nucleic Acids Res 39:6679-91. 2011
    ....
  5. 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...
  6. 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
    ....
  7. pmc Maintenance of the correct open reading frame by the ribosome
    Thomas M Hansen
    Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112 5330, USA
    EMBO Rep 4:499-504. 2003
    ..An earlier model for the decoding of this element proposed 'out-of-frame' binding of A-site tRNA without preceding P-site tRNA slippage...
  8. 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...
  9. pmc Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons
    Michael T Howard
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
    EMBO J 24:1596-607. 2005
    ..Sequences capable of forming strong RNA structures were also identified 3' adjacent to, or near, selenocysteine-encoding UGA codons in the Sps2, SelH, SelO, and SelT selenoprotein genes...
  10. 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...
  11. 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...
  12. pmc Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3
    Greg L Christensen
    Andrology and IVF Laboratories, University of Utah School of Medicine, Salt Lake City, UT, USA
    BMC Med Genet 7:27. 2006
    ..Ornithine decarboxylase antizyme 3 (OAZ3) is a testis-specific antizyme paralog and the only antizyme expressed in the mid to late stages of spermatogenesis...
  13. 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...
  14. ncbi request reprint A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene
    Norma M Wills
    Department of Human Genetics, 15 N 2030 E, Bldg 533, University of Utah, Salt Lake City, UT 84112, USA
    J Biol Chem 281:7082-8. 2006
    ..Although the functions of the Ma genes are unknown, the serious neurological effects of ectopic expression in tumor cells indicate their importance in the brain...
  15. ncbi request reprint Programmed ribosomal frameshifting in decoding the SARS-CoV genome
    Pavel V Baranov
    Department of Human Genetics, University of Utah, 15 N 2030 E, Room 7410, Salt Lake City, UT 84112 5330, USA
    Virology 332:498-510. 2005
    ..These results demonstrate key sequences required for efficient frameshifting, and the utility of mass spectrometry to study ribosomal frameshifting...
  16. ncbi request reprint Sequencing and haplotype analysis of the activator of CREM in the testis (ACT) gene in populations of fertile and infertile males
    Greg L Christensen
    Andrology and IVF Laboratories, University of Utah School of Medicine, Salt Lake City, 84108, USA
    Mol Hum Reprod 12:257-62. 2006
    ..We identified one ACT haplotype that had a 45% reduction in its interaction with CREM. Our results suggest that different haplotypes within the ACT gene may contribute to male factor subfertility...
  17. ncbi 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...
  18. 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...
  19. 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...
  20. ncbi request reprint P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation
    Douglas J Bucklin
    Department of Human Genetics, University of Utah, 15N 2030E Rm7410, Salt Lake City, UT 84112 5330, USA
    J Mol Biol 345:39-49. 2005
    ..The wild-type, GGA, matched codons are the most efficient in their gene 60 context in contrast to the relatively low value in the non-programmed bypassing study...
  21. pmc Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
    Olga Matveeva
    Department of Human Genetics, University of Utah, Salt Lake City 84112 5330, USA
    Nucleic Acids Res 35:e63. 2007
    ..It is available as a web tool called 'siRNA scales'...
  22. ncbi request reprint Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines
    Lorin M Petros
    Department of Human Genetics, University of Utah, 15 N 2030 E, Rm 7410, Salt Lake City, UT 84112 5330, USA
    J Biochem 140:657-66. 2006
    ..The impact of the xylene moiety and the distance between the positively charged amino groups on antizyme frameshifting and cell growth are discussed...
  23. pmc Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA
    Norma M Wills
    Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
    EMBO J 27:2533-44. 2008
    ..Dissipation of this RNA structure, together with the contribution of 16S rRNA anti-Shine-Dalgarno sequence pairing with GAG, facilitates peptidyl-tRNA re-pairing to mRNA...
  24. pmc Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli
    Olga L Gurvich
    Department of Human Genetics, University of Utah, 15N 2030E Salt Lake City, UT 84112 5330, USA
    EMBO J 22:5941-50. 2003
    ..The unexpected conclusion is that moderate frameshifting during expression of at least some other genes is not sufficiently harmful for cells to trigger strong negative evolutionary pressure...
  25. pmc RECODE 2003
    Pavel V Baranov
    Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112 5330, USA
    Nucleic Acids Res 31:87-9. 2003
    ..The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information. The Database is freely available at http://recode.genetics.utah.edu/...
  26. pmc P-site tRNA is a crucial initiator of ribosomal frameshifting
    Pavel V Baranov
    Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112 5330, USA
    RNA 10:221-30. 2004
    ..This model offers an alternative explanation to previously published mechanisms of programmed frameshifting, such as out-of-frame tRNA binding, and a different perspective on simultaneous tandem tRNA slippage...
  27. 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...
  28. 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
    ....
  29. pmc Observation of dually decoded regions of the human genome using ribosome profiling data
    Audrey M Michel
    Biochemistry Department, University College Cork, Ireland
    Genome Res 22:2219-29. 2012
    ....
  30. pmc Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli
    Olga L Gurvich
    Department of Human Genetics, University of Utah, 15N 2030E, Rm 7410, Salt Lake City, Utah 84112 5330, USA
    J Bacteriol 187:4023-32. 2005
    ..Thus, +1 frameshifting efficiency at AGG_AGG and AGA_AGA is influenced by the mRNA expression level. These tandem rare codons do not occur in highly expressed mRNAs...
  31. ncbi request reprint Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility
    Vincent W Aoki
    Andrology and IVF Laboratories, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
    Fertil Steril 86:1416-22. 2006
    ....
  32. ncbi request reprint Polyamine sensing during antizyme mRNA programmed frameshifting
    Lorin M Petros
    Department of Human Genetics, University of Utah, 15 N 2030 E, Rm 7410, Salt Lake City, UT 84112 5330, USA
    Biochem Biophys Res Commun 338:1478-89. 2005
    ..We also demonstrate that polyamines are required to stimulate stop codon readthrough at the MuLV redefinition site required for normal expression of the GagPol precursor protein...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. ncbi request reprint Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia
    Greg L Christensen
    University of Utah Andrology and IVF Laboratories, 675 Arapeen Drive, Suite 205, Salt Lake City, UT 84108, USA
    J Androl 27:11-5. 2006
  38. ncbi request reprint Novel antizyme gene in Danio rerio expressed in brain and retina
    Ivaylo P Ivanov
    Department of Human Genetics, University of Utah, Utah 84112 5330, United States
    Gene 387:87-92. 2007
    ..In addition to the retina, it is also expressed in the brain and somites...
  39. 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...
  40. 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...
  41. ncbi request reprint Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species
    Ivaylo P Ivanov
    Department of Human Genetics, University of Utah, 15N 2030E Rm 7410, Salt Lake City, UT 84112 5330, USA
    J Mol Biol 339:495-504. 2004
    ..Identification of the 3' frameshifting stimulator in intermediate species or other invertebrates remains unresolved...
  42. 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'...
  43. 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...
  44. pmc Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production
    Andrew E Firth
    Department of Pathology, University of Cambridge, Cambridge, UK
    J Gen Virol 92:1097-106. 2011
    ..These defects, which could be partially complemented in ORF5a-expressing cells, indicate that the novel protein, which may be the eighth structural protein of arteriviruses, is expressed and important for arterivirus infection...
  45. ncbi request reprint Computational identification of putative programmed translational frameshift sites
    Atul A Shah
    Department of Human Genetics, University of Utah, SLC, 84112 5330, USA
    Bioinformatics 18:1046-53. 2002
    ..cerevisiae preliminary to the laboratory testing of the most highly underrepresented oligos for frameshifting efficiency...
  46. 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...
  47. 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...
  48. ncbi request reprint Readthrough of dystrophin stop codon mutations induced by aminoglycosides
    Michael T Howard
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
    Ann Neurol 55:422-6. 2004
    ..Readthrough levels do not substantially vary between different sources of gentamicin, and, for this set of mutations, the efficiency of termination at the premature stop codon mutation does not appear to correlate with disease severity...
  49. pmc Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome
    Olga V Matveeva
    Department of Human Genetics, University of Utah, Salt Lake City 84112 5330, USA
    BMC Bioinformatics 5:44. 2004
    ..There is a need to develop software that will employ thermodynamic selection criteria for finding optimal hybridization targets in related sequences...
  50. pmc An overlapping essential gene in the Potyviridae
    Betty Y W Chung
    Biosciences Institute, University College Cork, Cork, Ireland
    Proc Natl Acad Sci U S A 105:5897-902. 2008
    ....
  51. ncbi request reprint Recoding: translational bifurcations in gene expression
    Pavel V Baranov
    Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112 5330, USA
    Gene 286:187-201. 2002
    ..This review deals with the function and distribution of recoding with a focus on the ribosomal frameshifting used for gene expression in bacteria...
  52. 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...
  53. 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...
  54. pmc Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
    Virag Sharma
    School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
    Nucleic Acids Res 42:7210-25. 2014
    ..The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting. ..
  55. 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...
  56. pmc Release factor 2 frameshifting sites in different bacteria
    Pavel V Baranov
    Department of Human Genetics, University of Utah, 15N 2030E Room 7410, Salt Lake City, UT 84112 5330, USA
    EMBO Rep 3:373-7. 2002
    ..Internal translation initiation occurs at the shift site, but any functional role is obscure...
  57. pmc Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides
    Michael T Howard
    Department of Human Genetics, University of Utah, 15 N 2030 E, Rm 7410, Salt Lake City, UT 84112 5330, USA
    RNA 10:1653-61. 2004
    ..The implications for the mechanism of action of natural programmed translational frameshift stimulators are discussed...
  58. ncbi request reprint Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice
    Alan J Herr
    Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112 5330
    J Biol Chem 279:11081-7. 2004
    ..The bacteriophage T4 gene 60 nascent peptide, known to influence take-off in its native context, imposes stringent P-site pairing requirements, thereby limiting the number of suitable landing sites...
  59. 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'...
  60. 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...
  61. pmc Artificial neural network prediction of antisense oligodeoxynucleotide activity
    Michael C Giddings
    Department of Human Genetics, University of Utah, SLC, UT 84112, USA and Isis Pharmaceuticals, Carlsbad, CA 92008, USA
    Nucleic Acids Res 30:4295-304. 2002
    ..Given an RNA transcript as input, the system identifies the most likely oligo targets and provides estimates of the probabilities that oligos targeted against these sites will be effective...
  62. pmc The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases
    Norma M Wills
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
    RNA 12:1149-53. 2006
    ..Antibiotics that affect mammalian ribosomes may have complex effects on frameshifting and disease progression...
  63. ncbi request reprint Biochemistry. The 22nd amino acid
    John F Atkins
    Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 5330, USA
    Science 296:1409-10. 2002