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Series GSE63789 Query DataSets for GSE63789
Status Public on Jan 05, 2015
Title Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Ribosome profiling data reports on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation.
Overall design We test whether tRNA abundance affects elongation or translation efficiency by changing the tRNA levels through deletion or over expression and measuring the ribosomal dwell time at each codon using a robust statistical method that accounts for flow conservation.
Contributor(s) Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D
Citation(s) 25538139
Submission date Dec 02, 2014
Last update date May 15, 2019
Contact name Cristina Pop
Organization name Stanford University
Department Computer Science
Street address 353 Serra Mall
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
Samples (10)
GSM1557442 WT mrna
GSM1557443 ACA-K mrna
GSM1557444 WT-URA mrna
BioProject PRJNA269069
SRA SRP050443

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63789_counts_ACA_K.txt.gz 1.3 Mb (ftp)(http) TXT
GSE63789_counts_AGG_OE_URA.txt.gz 1.1 Mb (ftp)(http) TXT
GSE63789_counts_AGG_QC_URA.txt.gz 996.9 Kb (ftp)(http) TXT
GSE63789_counts_wt.txt.gz 1.5 Mb (ftp)(http) TXT
GSE63789_counts_wt_URA.txt.gz 1.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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