ArticleBMC genomics2013
Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 101 citations in OpenAlex.
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- Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.Frontiers in immunology · 2025Review
- HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights.Briefings in bioinformatics · 2024Article
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- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs.Nature communications · 2024Article
- Integrated sequence and -omic features reveal novel small proteome ofFrontiers in microbiology · 2024Article
- A vast evolutionarily transient translatome contributes to phenotype and fitness.Cell systems · 2023Article
- Upstream open reading frames regulate translation of cancer-associated transcripts and encode HLA-presented immunogenic tumor antigens.Cellular and molecular life sciences : CMLS · 2022Article
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- Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.PLoS genetics · 2021Article
- Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens.Communications biology · 2021Article
- The role of micropeptides in biology.Cellular and molecular life sciences : CMLS · 2021Review
- Small Open Reading Frames, How to Find Them and Determine Their Function.Frontiers in genetics · 2021Review
- Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome.Bioinformatics (Oxford, England) · 2020Article
- Polycysteine-encoding leaderless short ORFs function as cysteine-responsive attenuators of operonic gene expression in mycobacteria.Molecular microbiology · 2020Article
- MetaRibo-Seq measures translation in microbiomes.Nature communications · 2020Article
- OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques.Database : the journal of biological databases and curation · 2020Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt 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.
resultsUsing 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.
conclusionOur 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.