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Open Access Highly Accessed Research article

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

Jeroen Crappé1*, Wim Van Criekinge1, Geert Trooskens1, Eisuke Hayakawa2, Walter Luyten3, Geert Baggerman4 and Gerben Menschaert1*

Author Affiliations

1 Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium

2 Research Group of Functional Genomics and Proteomics, KU Leuven, 3000 Leuven, Belgium

3 Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium

4 VITO Nv, 2400 Mol, Belgium – CFP, Center For Proteomics, 2020 Antwerpen, Belgium

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BMC Genomics 2013, 14:648  doi:10.1186/1471-2164-14-648

Published: 23 September 2013

Abstract

Background

It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e.g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs.

Results

Using bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides.

Conclusion

Our combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides.

Keywords:
Micropeptide; Small open reading frame; Mus musculus; Genome-wide; Ribosome profiling; LincRNA; sORF; ncRNA; Bioactive peptide