Transcriptomics

Dataset Information

296

Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells


ABSTRACT: 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. We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.

ORGANISM(S): Homo sapiens  

SUBMITTER: Gong Zhang   Jingjie Jin  Jiayong Zhong  Wei Gu  Xinlei Lian  Tong Wang  Yizhi Cui  Jiahui Guo 

PROVIDER: E-GEOD-46613 | ArrayExpress | 2016-02-09

SECONDARY ACCESSION(S): GSE46613SRP022049PRJNA201228

REPOSITORIES: GEO, ArrayExpress, ENA

Similar Datasets

2014-02-18 | E-GEOD-48603 | ArrayExpress
2014-02-18 | E-GEOD-49994 | ArrayExpress
2019-05-24 | PXD013051 | Pride
| GSE81269 | GEO
2014-06-10 | E-GEOD-58321 | ArrayExpress
| GSE109652 | GEO
2012-04-01 | GSE35641 | GEO
2012-04-01 | E-GEOD-35641 | ArrayExpress
2015-01-05 | E-GEOD-63789 | ArrayExpress
2013-03-05 | E-GEOD-42006 | ArrayExpress