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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
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Bi-directional ribosome scanning controls the stringency of start codon selection
Yifei Gu1, Yuanhui Mao1, Longfei Jia1
1Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA.
Nature Communications
|November 16, 2021
Summary
Ribosomes can scan backward along messenger RNA to find start codons, challenging the traditional unidirectional model. This discovery in protein synthesis highlights the role of RNA helicase eIF4A in regulating this process.
Area of Science:
- Molecular Biology
- Protein Synthesis
- Gene Expression Regulation
Background:
- Eukaryotic translation initiation traditionally assumes unidirectional 5'→3' scanning of the pre-initiation complex (PIC) along the 5' untranslated region (UTR).
- Accurate start codon recognition is critical for proper protein synthesis fidelity.
Purpose of the Study:
- To investigate translation initiation mechanisms, particularly with ultra-short 5' UTRs.
- To explore the role of pre-initiation complex (PIC) scanning directionality and the influence of RNA helicases.
Main Methods:
- Probing translation initiation using ultra-short 5' UTRs.
- Transcriptome-wide PIC profiling to identify ribosome footprints.
- Depletion and activity enhancement of the RNA helicase eIF4A.
Main Results:
- Identified AUG triplet selection via PIC backsliding in ultra-short 5' UTRs, indicating bi-directional scanning.
- Observed oscillation patterns in PIC footprints near the 5' end and start codons.
- Demonstrated that eIF4A depletion reduces PIC oscillations and upstream start codon selection, while enhanced activity promotes nonlinear scanning.
Conclusions:
- The pre-initiation complex can exhibit bi-directional scanning, including backsliding, challenging the established unidirectional model.
- The RNA helicase eIF4A plays a crucial role in regulating PIC scanning dynamics and start codon selection.
- A helicase-mediated PIC conformational switch may unify ribosome recruitment, scanning, and start codon selection processes.
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