Presentation Type

Poster

Faculty Mentor’s Full Name

Travis Wheeler

Faculty Mentor’s Department

Computer Science

Abstract

Enabled by a growing understanding of its genetic origins, modern medicine is increasingly moving towards prevention rather than treatment of disease. Notable innovations, such as genome editing, can impact medicine only in the context of extensive knowledge of human genetics. Yet it was recently discovered that a phenomenon called “alternative reading frame” (ARF) genes appears in the human genome far more commonly than was thought possible. Exons, the coding portion of DNA, are transcribed into RNA sequences consisting of groupings of three nucleotides called codons. Codons correspond to particular amino acids, and the chain of translated amino acids form a protein based on which exons are included. Unlike non-ARF genes, in ARFs one exon region can encode more than one protein sequence, depending on where the cell establishes the exon’s boundary. Because amino acids are encoded in the base-three codons, shifting the reading frame over by one or two nucleotides can cause dramatic changes in the encoded protein. This research seeks to confirm the existence of ARFs and identify the conditions under which they occur. To accomplish this, RNA sequences were downloaded from trusted databases and a combination of preexisting tools and custom scripts programmed in Perl were used to test for the occurrence of putative ARF sequences. Those RNA sequences found to contain ARFs were then analyzed to determine whether there was a pattern of occurrence. The results of this analysis will assist in filling a significant gap in our knowledge of how the human genome functions. If particular ARFs can be identified as having a relationship with the development of specific diseases, the impact on the medical field would be significant.

Category

Life Sciences

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Apr 27th, 3:00 PM Apr 27th, 4:00 PM

Quantifying the Presence of Alternative Reading Frames in the Human Genome

UC South Ballroom

Enabled by a growing understanding of its genetic origins, modern medicine is increasingly moving towards prevention rather than treatment of disease. Notable innovations, such as genome editing, can impact medicine only in the context of extensive knowledge of human genetics. Yet it was recently discovered that a phenomenon called “alternative reading frame” (ARF) genes appears in the human genome far more commonly than was thought possible. Exons, the coding portion of DNA, are transcribed into RNA sequences consisting of groupings of three nucleotides called codons. Codons correspond to particular amino acids, and the chain of translated amino acids form a protein based on which exons are included. Unlike non-ARF genes, in ARFs one exon region can encode more than one protein sequence, depending on where the cell establishes the exon’s boundary. Because amino acids are encoded in the base-three codons, shifting the reading frame over by one or two nucleotides can cause dramatic changes in the encoded protein. This research seeks to confirm the existence of ARFs and identify the conditions under which they occur. To accomplish this, RNA sequences were downloaded from trusted databases and a combination of preexisting tools and custom scripts programmed in Perl were used to test for the occurrence of putative ARF sequences. Those RNA sequences found to contain ARFs were then analyzed to determine whether there was a pattern of occurrence. The results of this analysis will assist in filling a significant gap in our knowledge of how the human genome functions. If particular ARFs can be identified as having a relationship with the development of specific diseases, the impact on the medical field would be significant.