18.01.09 Nonsense mediated decay Flashcards Preview

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What are mRNA surveillance mechanisms?

RNA surveillance mechanisms are methods cells use to assure the quality and fidelity of mRNA molecules, thus protecting against the accumulation of nonfunctional RNA and the subsequent production of abnormal peptides.

This is generally achieved through marking aberrant mRNA molecules for degradation by various endogenous nucleases.


What are the three mRNA surveillance mechanisms known to function within cells?

1. Nonsense Mediated mRNA decay pathway (NMD)
2. Nonstop Mediated mRNA decay pathways (NSD)
3. No-go Mediated mRNA decay pathway (NGD).


Describe no-go decay (NGD). What triggers NGD?

No-Go decay (NGD) is the most recently discovered surveillance mechanism and it is not currently well understood.

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 nonstop mediated decay (NSD)?

Nonstop Mediated decay (NSD) is involved in the detection and decay of mRNA transcripts which lack a stop codon.


How might mRNA trasncripts without stop codons arise? Why is this an issue for cells?

From many different mechanisms such as:
1. premature 3’ adenylation
2. cryptic polyadenylation signals within the coding region of a gene.

This lack of a stop codon results a significant issue for cells. Ribosomes translating the mRNA eventually translate into the 3’poly-A tail region of transcripts and stalls. As a result it cannot eject the mRNA.

Ribosomes thus may become sequestered associated with the nonstop mRNA and would not be available to translate other mRNA molecules into proteins. Nonstop mediated decay mediates this problem by both freeing the stalled ribosomes and marking the nonstop mRNA for degradation in the cell by nucleases. Nonstop mediated decay consists of two distinct pathways which likely act in concert to decay nonstop mRNA.


What is the nonsense mediate mRNA decay pathway (NMD)?

Regulatory mechanism targeting transcripts containing premature termination codons (PTCs; or nonsense (STOP) codons).


Why is it necessary to degrade mRNA transcripts containing PTCs?

Avoid the translation of proteins that may have dominant negative or gain of function activity. Failure to recognise and decay these mRNA transcripts can result in the production of truncated proteins which may be harmful to the organism.


What mechanisms can lead to the formation of a PTC?

1. Germline mutations in DNA
2. Somatic mutations in DNA
3. Errors in transcription
4. Errors in post transcriptional mRNA processing.


How does NMD have a role in maintaining the quality of the cell's transcriptome?

Approximately 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.


What proportion of known disease-associated mutations are estimated to be due to mRNAs containing PTCs?



How does NMD have a role in the physiological regulation of gene expression?

Controlling directly or indirectly the presence or abundance of up to 10% of all mRNAs as demonstrated by NMD ablation studies


Give examples of how NMD has a role in the physiological regulation of gene expression?

NMD has been shown to target
non-functional pseudogenes
transposable elements
long terminal repeats
mRNAs with reading frames in the 5'UTR and those that have escaped nuclear retention.


Summarise the key features of the PTC recognition mechanism

1) Important it only recognises a PTC, not a normal TC
2) Nt more than 50-54 nt upstream of the last exon-exon junction, marked by EJCs, can target mRNA for decay