Nonsense mediated mRNA decay (NMD) Flashcards
Types of mRNA surveillance mechanisms?
Nonstop Mediated decay (NSD)
No-Go decay (NGD)
Nonsense Mediated Decay (NMD)
What is Nonstop Mediated decay (NSD)?
Detection and decay of mRNA transcripts which lack a stop codon.
These transcripts arise from different mechanisms such as premature 3’ adenylation and cryptic polyadenylation signals within the coding region of a gene.
Ribosomes translating the mRNA eventually translate into the 3’poly-A tail region of transcripts and stalls and can therefore not eject the mRNA.
What is No-Go decay (NGD)?
Targets of NGD appear to consist largely of mRNA transcripts on which ribosomes have stalled during translation.
This stall can be caused by a variety of factors including strong secondary structures, which may physically block the translational machinery from moving down the transcript
What is Nonsense Mediated Decay (NMD)?
NMD targets transcripts containing PTCs which may arise through germline variants in DNA, somatic variants in DNA, errors in transcription, or errors in post transcriptional mRNA processing. By causing decay of C-terminally truncated polypeptides, the NMD mechanism can protect cells against deleterious dominant-negative, and gain of function effects. Failure to recognize and decay these mRNA transcripts can result in the production of truncated proteins which may be harmful to the organism.
Is NMD common?
60-70% of human pre-mRNAs are alternatively spliced and of these ~45% are predicted to have at least one spliced form that is targeted by NMD. Thus NMD has a major role in quality control of the cell’s transcriptome.
What percentage of disease associated mutations are targeted for NMD?
It is estimated that 30% of known disease-associated mutations are due to mRNAs containing PTCs.
How do premature translation termination codons (PTC) arise?
PTCs may also arise through programmed DNA rearrangements, for example in the T-cell Receptor and immunoglobulin genes whereby gene rearrangement is used to increase the repertoire of antigen receptors. During DNA recombination in these processes, PTCs are generated two thirds of the time, therefore this mRNA is targeted for degradation. Recombination then takes place on the 2nd allele to enable another attempt at producing a functioning protein. If the second recombination attempt results in a PTC, then the cell undergoes apoptosis.
How does NMD regulate gene expression?
by controlling directly or indirectly the presence or abundance of up to 10% of all mRNAs as demonstrated by NMD ablation studies.
eg. NMD was shown to target non-functional pseudogenes, transposable elements or long terminal repeats (LTRs), mRNAs with reading frames in the 5’UTR and those that have escaped nuclear retention
How does NMD regulate many physiological mRNAs?
~40% of mammalian mRNAs have an upstream ORF (uORF). An example is the Activating transcriptor factor 4 (ATF4), which is part of the integrated stress response. It has been suggested that under normal conditions translation from a 3 codon upstream ORF is followed by re-initiation at a 2nd non-functional uORF which is NMD sensitive. Under conditions of stress a standard ORF is used instead as the 2nd initiation site, and ATF4 mRNA is retained.
How is NMD involved in neuronal development?
In neuronal development high NMD activity in undifferentiated neuronal stem-like cells maintains their proliferative stem-like state, whereas reduction of NMD activity is crucial for their differentiation into neurons; downregulation of NMD factors UPF1 and UPF3B during neuronal development is controlled by a set of miRNAs that are upregulated in response to neuronal differentiation signals.
When is NMD predicted to occur?
A PTC must be recognized as different from a normal stop codon so that only the former triggers a NMD response. The predicted impact of a PTC depends on the location of the PTC within the transcript. In general, NMD is not predicted to occur if the premature termination codon occurs in the 3’ most exon or within the 3’-most 50 nucleotides of the penultimate exon
What are Exon junction complexes (EJCs)?
EJCs are multiprotein complexes that assemble during splicing at a position about 20-24 nucleotides upstream from the splice junction, marking the exon-exon boundary. They mark the sites where the introns were spliced out.
How are EJCs involved in NMD?
EJCs provide position information needed to discriminate premature stop codons from natural stop codons. The ribosome, as it traverses the mRNA, displaces any EJCs in its path. Upon arrival at the termination codon, release factors interact with any undisplaced EJCs. This association triggers decapping of the transcript, followed by degradation.
Is the spliceosome involved in NMD?
Recognition of PTCs appears to be dependent on the definitions of the exon-exon junctions and this suggests involvement of the spliceosome in mammalian NMD. Furthermore, it has been observed that NMD mechanisms are not activated by nonsense transcripts that are generated from genes that naturally do not contain introns
Function of major NMD components
During the processing of mammalian pre-mRNA, introns are excised and marked by a multiprotein EJC. When the translation complex pauses at a PTC that is upstream of an EJC, eukaryotic release factors recruit the RNA helicase UPF1, a vital component of the NMD mechanism. UPF1 then associates with UPF2, a component of the EJC, and is phosphorylated at several sites by SMG1. Phosphorylated UPF1 recruits SMG7 and SMG5, two 14-3-3 proteins that each bind to UPF1 and form a heterodimer, and results in the dephosphorylation of UPF-1 by PP2A. The phosphorylation and dephosphorylation of UPF1 are necessary steps before the degradation of the transcript by exonucleases.
