ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

Autor: Hazarika RR; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium., De Coninck B; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.; Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, B-9052, Belgium., Yamamoto LR; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium., Martin LR; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium., Cammue BP; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.; Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, B-9052, Belgium., van Noort V; KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium. vera.vannoort@kuleuven.be.
Jazyk: angličtina
Zdroj: BMC bioinformatics [BMC Bioinformatics] 2017 Jan 17; Vol. 18 (1), pp. 37. Date of Electronic Publication: 2017 Jan 17.
DOI: 10.1186/s12859-016-1458-y
Abstrakt: Background: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana.
Results: To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides.
Conclusion: To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.
Databáze: MEDLINE
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