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Aberrant mRNAs with extended 3' UTRs are substrates for rapid degradation by mRNA surveillance
1Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson 85721, USA.
Abstract:
The mRNA surveillance system is known to rapidly degrade aberrant mRNAs that contain premature termination codons in a process referred to as nonsense-mediated decay. A second class of aberrant mRNAs are those wherein the 3' UTR is abnormally extended due to a mutation in the polyadenylation site. We provide several observations that these abnormally 3'-extended mRNAs are degraded by the same machinery that degrades mRNAs with premature nonsense codons. First, the decay of the 3'-extended mRNAs is dependent on the same decapping enzyme and 5'-to-3' exonuclease. Second, the decay is also dependent on the proteins encoded by the UPF1, UPF2, and UPF3 genes, which are known to be specifically required for the rapid decay of mRNAs containing nonsense codons. Third, the ability of an extended 3' UTR to trigger decay is prevented by stabilizing sequences within the PGK1 coding region that are known to protect mRNAs from the rapid decay induced by premature nonsense codons. These results indicate that the mRNA surveillance system plays a role in degrading abnormally extended 3' UTRs. Based on these results, we propose a model in which the mRNA surveillance machinery degrades aberrant mRNAs due to the absence of the proper spatial arrangement of the translation-termination codon with respect to the 3' UTR element as defined by the utilization of a polyadenylation site.
Insights
Aberrant messenger RNAs (mRNAs) with extended 3' untranslated regions (UTRs) are degraded by the same nonsense-mediated decay machinery. This surveillance system ensures proper mRNA quality control by targeting faulty transcripts.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Messenger RNA (mRNA) quality control is crucial for cellular function.
- Nonsense-mediated decay (NMD) degrades aberrant mRNAs with premature termination codons.
- Alternative mRNA degradation pathways for other aberrant transcripts are less understood.
Purpose of the Study:
- To investigate whether the mRNA surveillance system degrades mRNAs with abnormally extended 3' untranslated regions (UTRs).
- To determine if the machinery involved in nonsense-mediated decay also targets 3'-extended mRNAs.
Main Methods:
- Comparative analysis of mRNA decay rates.
- Assays for decapping enzyme and exonuclease activity.
- Genetic analysis using UPF1, UPF2, and UPF3 gene knockdowns.
- Functional studies involving stabilizing sequences in the PGK1 coding region.
Main Results:
- Decay of 3'-extended mRNAs requires the same decapping enzyme and 5'-to-3' exonuclease as NMD.
- UPF1, UPF2, and UPF3 proteins are essential for the degradation of 3'-extended mRNAs.
- Stabilizing sequences in the PGK1 coding region inhibit the decay of 3'-extended mRNAs, similar to their effect on NMD targets.
Conclusions:
- The mRNA surveillance system degrades aberrant mRNAs with abnormally extended 3' UTRs.
- This degradation process utilizes the same molecular machinery as nonsense-mediated decay.
- A proposed model suggests that aberrant mRNA degradation is triggered by the misplacement of translation-termination codons relative to 3' UTR elements.