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Updated: Mar 31, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner
Min Shi1, Heng Zhang1, Lantian Wang1
1State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Premature termination codons (PTCs) in messenger RNAs (mRNAs) trigger nuclear retention, not degradation. Ribosomes in the nucleus detect PTCs, recruiting Upf1 protein to hold faulty mRNAs, ensuring protein production fidelity.
Area of Science:
- Molecular Biology
- Cell Biology
- Genetics
Background:
- Nonsense-mediated mRNA decay (NMD) typically degrades mRNAs with premature termination codons (PTCs).
- PTCs signal the presence of errors in mRNA sequences.
Purpose of the Study:
- To investigate the fate of mRNAs containing premature termination codons (PTCs).
- To elucidate the mechanism of nuclear retention for PTC-containing mRNAs.
Main Methods:
- Analysis of mRNA localization in the nucleus and cytoplasm.
- Investigation of ribosome-mRNA interactions within the nucleus.
- Study of the role of the Upf1 protein in mRNA processing.
Main Results:
- mRNAs with PTCs (UAA, UAG, UGA) are retained in the nucleus, unlike wild-type mRNAs.
- Nuclear retention of PTC-containing mRNAs is dependent on the reading frame.
- Translating ribosomes in the nucleus detect PTCs and recruit the Upf1 protein.
- Upf1 is essential for the nuclear retention of PTC-containing mRNAs.
Conclusions:
- PTCs are recognized in the nucleus by translating ribosomes, leading to Upf1 recruitment and nuclear mRNA retention.
- This nuclear proofreading mechanism adds a layer of quality control for mRNA.
- Nuclear PTC recognition is crucial for maintaining high fidelity in protein production.
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