Title
Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
Author
Faculty/Department
Faculty of Sciences. Biology
Publication type
article
Publication
London ,
Subject
Biology
Human medicine
Engineering sciences. Technology
Source (journal)
BMC genomics. - London
Volume/pages
14(2013) , 12 p.
ISSN
1471-2164
1471-2164
Article Reference
648
Carrier
E-only publicatie
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
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.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/c85ac6/9642.pdf
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