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Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress

Overview of attention for article published in BMC Genomics, August 2017
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Title
Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress
Published in
BMC Genomics, August 2017
DOI 10.1186/s12864-017-3996-8
Pubmed ID
Authors

Zhiwen Jiang, Jiaqi Yang, Aimei Dai, Yuming Wang, Wei Li, Zhi Xie

Abstract

Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of genome-wide studies have been largely focused on transcriptional changes of cells in response to hypoxia. Recently developed ribosome profiling provides an opportunity to study genome-wide translational changes. To gain systemic insights into the transcriptional and translational regulation of cellular in response to hypoxic stress, we used simultaneous RNA sequencing and ribosome profiling on an RPE cells line, ARPE-19, under hypoxia condition. Both HIF-1α and EPAS1 (HIF-2α) proteins were stabilized in ARPE-19 under hypoxic stress treatment at 1 h, 2 h and 4 h. Analysis of simultaneous RNA sequencing and ribosome profiling data showed genome-wide gene expression changes at both transcriptional and translational levels. Comparative analysis of ribosome profiling and RNA-seq data revealed that hypoxia induced changes of more genes at the translational than the transcriptional levels. Ribosomes densities at 5' untranslated region (UTR) significantly increased under hypoxic stress. Interestingly, the increase in ribosome densities at 5' UTR is positively correlated with the presence of upstream open reading frames (uORFs) in the 5' UTR of mRNAs. Our results characterized translational profiles of mRNAs for a RPE cell line in response to hypoxia. In particular, uORFs play important roles in the regulation of translation efficiency by affecting ribosomes loading onto mRNAs. This study provides the first attempt to understand translational response of mammalian cells under hypoxic condition.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 64 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 64 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 22%
Researcher 12 19%
Student > Master 8 13%
Student > Bachelor 7 11%
Student > Doctoral Student 5 8%
Other 4 6%
Unknown 14 22%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 31 48%
Agricultural and Biological Sciences 8 13%
Medicine and Dentistry 5 8%
Chemistry 2 3%
Computer Science 1 2%
Other 3 5%
Unknown 14 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 August 2017.
All research outputs
#17,913,495
of 22,999,744 outputs
Outputs from BMC Genomics
#7,611
of 10,692 outputs
Outputs of similar age
#227,739
of 317,628 outputs
Outputs of similar age from BMC Genomics
#129
of 206 outputs
Altmetric has tracked 22,999,744 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,692 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 23rd percentile – i.e., 23% of its peers scored the same or lower than it.
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We're also able to compare this research output to 206 others from the same source and published within six weeks on either side of this one. This one is in the 24th percentile – i.e., 24% of its contemporaries scored the same or lower than it.