Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.

Alexey A Gritsenko,Eran Segal,Ronit Nir,Shira Weingarten-Gabbay,Dick De Ridder,Shani Elias-Kirma,Donna K Slonim

doi:10.1371/journal.pcbi.1005734

Abstract

Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity. We present the first in-depth computational analysis of a large body of IRESs, exploring RNA sequence features predictive of IRES activity. We identified predictive k-mer features resembling IRES trans-acting factor (ITAF) binding motifs across human and viral IRESs, and found that their effect on expression depends on their sequence, number and position. Our results also suggest that the architecture of retroviral IRESs differs from that of other viruses, presumably due to their exposure to the nuclear environment. Finally, we measured IRES activity of synthetically designed sequences to confirm our prediction of increasing activity as a function of the number of short IRES elements.

Highlights

Translation of mRNA into protein is an essential step in the process of gene expression
We identified pyrimidine-rich sequence features resembling several known Internal Ribosome Entry Sites (IRESs) Trans-Acting Factor (ITAF) binding motifs as predictive across human and viral IRESs, and discovered that their effect on IRES activity is strongest at distinct positions upstream of the start codon
To explore the relationship between IRES sequence and activity, we described its primary sequence using numerical features which could be related to IRES activity by the learned Random Forests (RFs)

Summary

Introduction

Translation of mRNA into protein is an essential step in the process of gene expression. Once the AUG is found in a favourable context, the 60S ribosomal subunit is assembled on the mRNA to begin protein synthesis [1, 2] This translation initiation route accounts for more that 95% of cellular mRNAs [3], in a growing number cases alternative strategies are employed to initiate translation [4, 5]. IRESs were since discovered in other viruses, including HCV and HIV [7, 8, 9], in cellular genes such as p53 [10], XIAP [11] and Bcl-2 [12] They were shown to support the ongoing protein synthesis under conditions in which cap-dependent translation is inhibited, such as mitosis or cellular stress. Emerging evidence suggests that in addition to this “back-up” mechanism, cellular IRESs play important roles under conditions in which cap-dependent translation is intact: they facilitate the translation of different proteins from cellular bicistronic transcripts [16]; guide ribosomes to produce N-truncated isoforms from alternative downstream AUG codons [17, 18, 19]; and enable translation of transcripts with locally inhibited cap-dependent translation [20]

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Results

Discussion

Conclusion