jamespblloyd.bsky.social
Synthetic AstroBotatnist. Engineer of synthetic gene circuits in plants. 🇬🇧🇪🇺 now in 🇦🇺. He/They.
Google Scholar: http://shorturl.at/dnHVZ
Compbio blog: badgrammargoodsyntax.com
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We then tested if the new ORFs led to a change in interpretation of NMD target identification from public NMD-mutant data from Arabidopsis. Short answer: Yes. Long answer YEESSSSSS!!!
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
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We start by demonstrating that the commonly used Araport11 transcriptome for model plant Arabidopsis annotates the longest ORF of known NMD targets (internal M codon used as start after AS-NMD event). Their 3' UTRs look normal, so would be missed when looking for typical signs of an NMD target!
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Thank you and thank you!
(Really odd, thanks for posting this link!)
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I don't think this is just important for NMD: what if you used the wrong ORF annotation for an AlphaFold structure prediction? You would get a N-terminal truncation that would NEVER exist in the cell (so useless). In reality it would be a C-terminal truncation. So be careful!!!
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We finally show that splicing in the 3' UTR (PTC-dEJ in the paper) was easier to find and link to NMD targets when we used the revised ORF annotations.
So PLEASE re-annotate transcripts not with the longest ORF but the most biologically authentic one!
Also see:
academic.oup.com/plcell/artic...
comment in response to
post
We then tested if the new ORFs led to a change in interpretation of NMD target identification from public NMD-mutant data from Arabidopsis. Short answer: Yes. Long answer YEESSSSSS!!!
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
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We used TranSuite software to re-annotate the ORFs starting with the authentic start codon. This found the early stop codon (PTC) and highlighted the long, splicing-rich 3' UTR (full of NMD-stimulating features). Over 2000 transcripts in Araport11 were modified in a similar way.
comment in response to
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We start by demonstrating that the commonly used Araport11 transcriptome for model plant Arabidopsis annotates the longest ORF of known NMD targets (internal M codon used as start after AS-NMD event). Their 3' UTRs look normal, so would be missed when looking for typical signs of an NMD target!
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We developed CrossFilt, a read-level, cross-species filtering approach that avoids these errors without sacrificing usable data. It outperforms all existing strategies and exposes just how much signal in comparative genomics has been misread.
doi.org/10.1101/2025...
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Is anyone automatically making Ramachandran plot and spotting these via disallowed regions on the plot?
Disclaimer: not a protein biochemistry, but I teach about Ramachandran plots and I feel this is exactly what they are for!