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A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana

  • Qiwen Hu
  • Catharina Merchante
  • Anna N. Stepanova
  • Jose M. Alonso
  • Steffen Heber
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9096)

Abstract

Upstream open reading frames (uORFs) are open reading frames located within the 5’ UTR of an mRNA. It is believed that translated uORFs reduce the translational efficiency of the main coding region, and play an important role in gene regulation. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a stacking-based classification approach to identify translated uORFs in Arabidopsis thaliana. Our approach resulted in a set of 5360 potentially translated uORFs in 2051 genes. GO terms enriched in uORF-containing genes include gene regulation, signal transduction and metabolic pathway. The identified uORFs occur with a higher frequency in multi-isoform genes, and many uORFs are affected by alternative transcript start sites or alternative splicing events.

Keywords

uORF Translation Ribosome footprinting Stacking Classification Arabidopsis thaliana 

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Qiwen Hu
    • 1
  • Catharina Merchante
    • 2
  • Anna N. Stepanova
    • 2
  • Jose M. Alonso
    • 2
  • Steffen Heber
    • 1
  1. 1.Research CenterNorth Carolina State UniversityRaleighUSA
  2. 2.Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighUSA

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