A novel signature for identification of upstream alternative translation initiation sites

Kritika Karri, Dhundy R. Bastola

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Alternative translation initiation sites (aTIS) and the factors that determine an ideal mode of translation of mRNA in the eukaryotic system has been widely studied over the past several decades. Such studies demonstrate that single mRNA can yield multiple protein isoforms using the AUG and non-AUG start codons. While the conspicuous scanning model explains how the process of translation initiation begins when the pre-initiation complex encounters a start codon with optimal sequence context, referred to as "Kozak" consensus and the leaky scanning model explains the process of alternative translation downstream. Additionally, there are alternative translation initiation sites upstream and in-frame to the canonical AUG start site, which are present in the 5′ UTR of the mRNA. This choice of aTIS results in a longer N-terminally expanded protein isoform. It is unclear as to what are the factors that determine the selection of a start codon to be a potential upstream aTIS. In this study we investigate if there exists a third element, besides the sequence context at a certain distance from canonical AUG start codon, in the 5′ UTR of human mRNAs called the "complementary matching palindrome" that differentiates an upstream aTIS from any other codon. Our results show the presence of longest complementary matching palindrome around CUG codon, which may serve as an aTIS to translate proteins that are longer than their canonical isoforms.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1184-1191
Number of pages8
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Keywords

  • 5′ UTR
  • Complementary matching palindrome
  • aTIS (alternative Translation Initiation Site)
  • uORF

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

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  • Cite this

    Karri, K., & Bastola, D. R. (2015). A novel signature for identification of upstream alternative translation initiation sites. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1184-1191). [7359850] (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359850