10.6078/D1ZM39
Lloyd, James
0000-0002-4492-1368
University of Western Australia
French, Courtney
0000-0001-7620-1544
University of Cambridge
Brenner, Steven
University of California, Berkeley
Polysome fractionation analysis reveals features important for human
nonsense-mediated mRNA decay
Dryad
dataset
2019
2019-08-30T00:58:18Z
2019-08-30T00:58:18Z
en
303461842 bytes
1
Creative Commons Attribution 4.0 International (CC BY 4.0)
Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA
surveillance pathway that eliminates transcripts with premature
termination codons. Several studies have tried defined the features
governing which transcripts are targeted to NMD. However, these approaches
often rely on inhibiting core NMD factors, which often have roles in
non-NMD processes within the cell. Based on reports that NMD-targeted
transcripts are often bound by a single ribosome, we analyzed RNA-Seq data
from a polysome fractionation experiment (TrIP-Seq) to characterize the
features of NMD-targeted transcripts in human cells. This approach
alleviates the need to inhibit the NMD pathway. We found that the EJC
model, wherein an exon-exon junction located ≥50 nucleotides downstream of
a stop codon is predicted to elicit NMD, was a powerful predictor of
transcripts with high abundance in the monosome fraction (bound by a
single ribosome). This was also true for the presence of an upstream open
reading frame. In contrast, as 3’ UTR lengths increase, the proportion of
transcripts that are most abundant monosome fraction does not increase.
This suggests that either longer 3’ UTRs do not consistently act as potent
triggers of NMD or that the degradation of these transcripts is
mechanistically different to other NMD-targeted transcripts. Of the
ribosome-associated transcripts annotated as “non-coding”, we find that a
majority are bound by a single ribosome. Many of these transcripts
increase in response to NMD inhibition, including the oncogenic SHNG15,
suggesting many might be NMD targets. Finally, we found that retained
intron transcripts without a premature termination codon are
over-represented in the monosome fraction, suggesting an alternative
mechanism is responsible for the low level of translation of these
transcripts. In summary, our analysis finds that the EJC model is a
powerful predictor of NMD-targeted transcripts, while the presence of a
long 3’ UTR is not.