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| Title |
The role of nucleotide composition in premature termination codon recognition
|
|---|---|
| Published in |
BMC Bioinformatics, December 2016
|
| DOI | 10.1186/s12859-016-1384-z |
| Pubmed ID | |
| Authors |
Fouad Zahdeh, Liran Carmel |
| Abstract |
It is not fully understood how a termination codon is recognized as premature (PTC) by the nonsense-mediated decay (NMD) machinery. This is particularly true for transcripts lacking an exon junction complex (EJC) along their 3' untranslated region (3'UTR), and thus degrade through the EJC-independent NMD pathway. Here, we analyzed data of transcript stability change following NMD repression and identified over 200 EJC-independent NMD-targets. We examined many features characterizing these transcripts, and compared them to NMD-insensitive transcripts, as well as to a group of transcripts that are destabilized following NMD repression (destabilized transcripts). We found that none of the known NMD-triggering features, such as the presence of upstream open reading frames, significantly characterizes EJC-independent NMD-targets. Instead, we saw that NMD-targets are strongly enriched with G nucleotides upstream of the termination codon, and even more so along their 3'UTR. We suggest that high G content around the termination codon impedes translation termination as a result of mRNA folding, thus triggering NMD. We also suggest that high G content in the 3'UTR helps to activate NMD by allowing for the accumulation of UPF1, or other NMD-promoting proteins, along the 3'UTR. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 20 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 5% |
| Unknown | 19 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 9 | 45% |
| Student > Ph. D. Student | 3 | 15% |
| Other | 2 | 10% |
| Student > Bachelor | 2 | 10% |
| Student > Master | 2 | 10% |
| Other | 2 | 10% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 9 | 45% |
| Agricultural and Biological Sciences | 9 | 45% |
| Computer Science | 1 | 5% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | 5% |
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 08 December 2016.
All research outputs
#20,359,475
of 22,908,162 outputs
Outputs from BMC Bioinformatics
#6,880
of 7,305 outputs
Outputs of similar age
#353,668
of 419,655 outputs
Outputs of similar age from BMC Bioinformatics
#106
of 128 outputs
Altmetric has tracked 22,908,162 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,305 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 128 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.