#apaperaday: Post-transcriptional Regulation of Gene Expression via Unproductive Splicing
In today’s #apaperaday, Prof. Aartsma-Rus reads and comments on the paper titled: Post-transcriptional Regulation of Gene Expression via Unproductive Splicing
Splicing themed with a review paper from Zavileyskiy from Acta Naturae on post transcriptional regulation of transcripts via unproductive splicing. DOI: 10.32607/actanaturae.27337
Nonsense mediated decay (NMD) is a process where transcripts that do not code for a protein are broken down. The process is activated during translation of a transcript when the ribosomes spot a stop signal before an exon-exon junction signal.
The exon-exon junction signals are leftovers from the splicing process and they are removed during the first round of translation. As most often the stop signal is in the last exon, having exon-exon junction signals after a stop makes no sense (pun intended).
When this happens, UPF1 protein will initiate the degradation of the mRNA. There are also other mechanisms to achieve NMD AND there are of course ways to avoid it too. This is biology after all.
The NMD mechanism was thought to be in place to prevent waste of amino acids and translational machinery time on something not productive, but also to avoid the production of toxic, non-functional protein (always a risk).
However, it is now clear that many transcripts autoregulate protein levels by having transcript isoforms that will induce NMD. This is called regulated unproductive splicing and translation (RUST).
An example is RBM10, an RNA binding protein, that binds its OWN transcript and causes the skipping of 2 exons to then initiate NMD and stop the production of more RBM10.
The exon causing NMD is also called poison exon. It can induce a frame-shift or contain a stop signal. These exons can be mutually exclusive with other exons or just added in or be a coding exon that is skipped.
Finding the transcripts that actively undergo RUST is difficult as due to NMD they are short-lived so you will not see them (in high amounts) with sequencing. Some transcripts however escape NMD, e.g. those with a long last exon.
Furthermore, some transcripts with a stop in an in-frame poison exon will be translated either into full-length proteins (where the stop is ignored by the ribosomes) or by starting translation beyond the poison exon.
Unproductive splicing and NMD can also cause diseases. Authors give examples like Duchenne and cystic fibrosis, but I would argue that these are not caused by unproductive splicing OR NMD, but rather because of the frame-shifting variants.
In other words, if there would be no NMD, the transcripts would still not code for a functional protein. I do agree with the authors flagging TANGO (targeted augmentation of nuclear genome output) using antisense oligonucleotides (ASOs) to skip poison exons.
Authors also mention Duchenne as an example of ASOs to restore productive splicing. They restore the reading frame – yes – but the resulting protein is only partially functional so this is not the same as TANGO where a normal protein is produced.
Finally, there are diseases where due to mutations the protein coding exon is not included, but the poison exon is included at increased levels. Here ASOs might restore normal splicing. I enjoyed reading the review, as it is not a regular focus.
