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


CONCLUSIONS
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.
Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium. Jeroen.Crappe@Ugent.be.
Jeroen
J
Crappé
Wim
W
Van Criekinge
Geert
G
Trooskens
Eisuke
E
Hayakawa
Walter
W
Luyten
Geert
G
Baggerman
Gerben
G
Menschaert
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D021901:DNA, Intergenic / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism; D016678:Genome / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D010455:Peptides / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D015203:Reproducibility of Results; D012270:Ribosomes / Q000235:genetics*; D016415:Sequence Alignment
D021901:DNA, Intergenic; D010455:Peptides; D022661:RNA, Untranslated