July 2019
Volume 60, Issue 9
Open Access
ARVO Annual Meeting Abstract  |   July 2019
Identification of a new Kozak consensus in genes expressed in photoreceptors.
Author Affiliations & Notes
  • Anum Butt
    Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
    Oxford Eye Hospital, United Kingdom
  • Michelle E McClements
    Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
    Oxford Eye Hospital, United Kingdom
  • Robert E MacLaren
    Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
    Oxford Eye Hospital, United Kingdom
  • Footnotes
    Commercial Relationships   Anum Butt, None; Michelle McClements, None; Robert MacLaren, None
  • Footnotes
    Support  None
Investigative Ophthalmology & Visual Science July 2019, Vol.60, 3399. doi:
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      Anum Butt, Michelle E McClements, Robert E MacLaren; Identification of a new Kozak consensus in genes expressed in photoreceptors.. Invest. Ophthalmol. Vis. Sci. 2019;60(9):3399.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : The Kozak consensus is a DNA sequence identified in eukaryotic genes that facilitates translation by identifying the start codon to ribosomes. Alterations to the Kozak consensus influence gene translational efficiency and can cause disease. The original Kozak consensus was defined by sequences identified in non-ocular tissues and, to date, the consensus for retinal genes remains unexplored. Knowledge of the Kozak sequence in retinal genes may be important in the design of adeno-associated viral (AAV) vectors for retinal gene therapy.

Methods : Data were compiled using the Geneious 10.0.9 software to review 26 human genes expressed in the retinal pigment epithelium (RPE) and 34 expressed in photoreceptor cells. Consensus nucleotides from position -12 to +4 around the translation initiator codon ATG were extracted for all genes. The ExAc database was used to identify known nucleotide variations at these positions. The conserved frequencies of nucleotides at positions -12 to +4 were determined and compared to those identified by Marilyn Kozak at the respective positions in 699 genes from vertebrates using an independent chi-square test per nucleotide position.

Results : The consensus nucleotides of RPE genes from positions -12 to +4 matched those of the original Kozak consensus presented in 1987. Comparisons of photoreceptor gene nucleotide frequencies revealed significant differences at positions -4 and -2 (p<0.0001 and p<0.007, respectively). In photoreceptor genes, 51% carried a G at position -4 whereas in 699 vertebrate genes, 15% contained the G nucleotide. In vertebrate genes, the majority (53%) carried a C at the -4 position with the next most common nucleotide being A (25%), which is in contrast to the preference for G at this position in photoreceptor genes. At the -2 position, nucleotide A was present in 41% of photoreceptor genes and 27% of vertebrate genes, the preference for which was C at the -2 position (49%). Of the 34 photoreceptor genes analysed, 29 carried nucleotides that differed to the original Kozak consensus at either the -4 or -2 position, or both.

Conclusions : The identification of a novel translation initiation consensus in photoreceptor genes offers a new insight into the regulation of expression of these genes and provides an opportunity to consider the Kozak consensus use in AAV gene therapy vectors that target these cells.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.

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