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| Status |
Public on Feb 09, 2016 |
| Title |
Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration.
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| Overall design |
We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.
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| Contributor(s) |
Lian X, Guo J, Gu W, Cui Y, Jin J, Zhong J, Zhang G, Wang T |
| Citation(s) |
26926465 |
| Submission date |
May 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Department |
Institute of Life and Health Engineering
|
| Lab |
Translatomics Lab
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA201228 |
| SRA |
SRP022049 |
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