Nakahigashi et al. 2016 (PRJDB2960)

General Details

Title Translation_profile_of_Ecoli_genes
Organism
Number of Samples 1
Release Date 2016/04/05 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA DRP003075
ENA DRP003075
GEO 0.0
BioProject PRJDB2960

Publication

Title
Authors Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H
Journal DNA research : an international journal for rapid publication of reports on genes and genomes
Publication Date 2016 Jun
Abstract Tetracycline-inhibited ribosome profiling (TetRP) provides a powerful new experimental tool for comprehensive genome-wide identification of translation initiation sites in bacteria. We validated TetRP by confirming the translation start sites of protein-coding genes in accordance with the 2006 version of Escherichia coli K-12 annotation record (GenBank U000962) and found ∼150 new start sites within 60 nucleotides of the annotated site. This analysis revealed 72 per cent of the genes whose initiation site annotations were changed from the 2006 GenBank record to the newer 2014 annotation record (GenBank U000963), indicating a high sensitivity. Also, results from reporter fusion and proteomics of N-terminally enriched peptides showed high specificity of the TetRP results. In addition, we discovered over 300 translation start sites within non-coding, intergenic regions of the genome, using a threshold that retains ∼2,000 known coding genes. While some appear to correspond to pseudogenes, others may encode small peptides or have previously unforeseen roles. In summary, we showed that ribosome profiling upon translation inhibition by tetracycline offers a simple, reliable and comprehensive experimental tool for precise annotation of translation start sites of expressed genes in bacteria. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
PMC PMC4909307
PMID 27013550
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
DRR021385 PRJDB2960 Escherichia coli 0.0 0.0 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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