Willems et al. 2016 (PRJNA348553)

General Details

Title N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.
Organism
Number of Samples 2
Release Date 2016/10/14 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP091588
ENA SRP091588
GEO GSE88790
BioProject PRJNA348553

Publication

Title
Authors Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, Van Breusegem F, Gevaert K, Van Damme P
Journal Molecular & cellular proteomics : MCP
Publication Date 2017 Jun
Abstract Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
PMC PMC5461538
PMID 28432195
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR4424237 PRJNA348553 Arabidopsis thaliana 0.0 Ribo-Seq Lactimidomycin
SRR4424238 PRJNA348553 Arabidopsis thaliana 0.0 Ribo-Seq Cycloheximide
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

ⓘ For more Information on the columns shown here see: About