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Series GSE80156 Query DataSets for GSE80156
Status Public on Apr 12, 2016
Title A coding sequence-embedded principle governs translational reading frame fidelity
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.
Overall design Investigating the role of 18S rRNA in controlling translational reading frame fidelity
Contributor(s) Wan J, Gao X, Mao Y, Dong L, Jia L, Zhang X, Qian S
Citation(s) 31549036
Submission date Apr 11, 2016
Last update date Oct 01, 2019
Contact name Ji Wan
Organization name Cornell University
Street address 303 Biotech 526 Campus Road
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM2113580 Ribo-Seq (HEK293 cells)
GSM2113581 Ribo-Seq (MEF cells)
GSM2113582 Ribo-Seq (MEF cells, WT 18S rRNA)
BioProject PRJNA318051
SRA SRP073116
SRA SRP073116

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Supplementary file Size Download File type/resource
GSE80156_RAW.tar 1.1 Gb (http)(custom) TAR (of TAR, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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