insight - Computational Biology - # eIF3-mediated mRNA circularization

eIF3 Binds to 3'-UTR Termini of Actively Translated mRNAs in Neural Progenitor Cells, Suggesting a Role in mRNA Circularization

Q: How does the role of eIF3 in mRNA circularization differ across various cell types and differentiation stages beyond early NPCs?

While the study focuses on early NPCs, the role of eIF3 in mRNA circularization likely exhibits cell type- and differentiation stage-specific variations. Here's why: Translational Landscape: Different cell types and differentiation stages possess unique translational landscapes, influenced by factors like transcription factor availability, RNA-binding protein expression, and signaling pathways. These factors can alter the repertoire of actively translated mRNAs, potentially impacting eIF3's 3'-UTR engagement and its role in circularization. eIF3 Subunit Composition: The eIF3 complex comprises 13 subunits, some of which exhibit tissue-specific expression and post-translational modifications. Variations in eIF3 subunit composition could influence its interactions with RNA and other proteins, potentially affecting its role in mRNA circularization in a cell type- and differentiation stage-dependent manner. Alternative Polyadenylation (APA): APA, a process generating mRNA isoforms with different 3'-UTR lengths, is highly regulated during development and differentiation. Since eIF3 interacts with 3'-UTR termini, variations in APA patterns across cell types and differentiation stages could influence eIF3's binding sites and its role in circularization. Crosstalk with Other Regulatory Mechanisms: mRNA circularization is a dynamic process influenced by multiple factors, including RNA modifications (e.g., m6A), RNA-binding proteins, and microRNAs. The interplay between these factors and eIF3's role in circularization likely varies across cell types and differentiation stages. Further research is needed to elucidate the precise mechanisms underlying these potential variations and their functional implications. Investigating eIF3's role in mRNA circularization across a broader range of cell types and differentiation stages will provide a more comprehensive understanding of its contribution to translational regulation.

Q: Could the observed eIF3 interaction with 3'-UTR termini be a consequence of ribosome stalling or quality control mechanisms rather than active translation?

While the study suggests a correlation between eIF3's 3'-UTR interaction and active translation, the possibility of ribosome stalling or quality control mechanisms contributing to this observation cannot be entirely ruled out. Here's why: Ribosome Stalling: Stalled ribosomes can trigger mRNA quality control pathways, potentially leading to the recruitment of eIF3 to the 3'-UTR. This recruitment could be part of a surveillance mechanism to assess the stalled ribosome or facilitate its rescue or disassembly. Nonsense-Mediated Decay (NMD): NMD is a quality control pathway targeting mRNAs with premature termination codons (PTCs). Ribosome stalling at PTCs can trigger NMD, and eIF3's presence at the 3'-UTR could be linked to this process. No-Go Decay (NGD): NGD targets mRNAs with strong stalls in the coding sequence. Similar to NMD, eIF3's 3'-UTR interaction could be associated with NGD-mediated mRNA degradation. However, several observations in the study argue against these possibilities: Correlation with Translation Levels: The study demonstrates a positive correlation between eIF3's 3'-UTR binding and ribosome occupancy, suggesting a link to active translation rather than solely stalling or quality control. Absence on Non-polyadenylated mRNAs: eIF3's 3'-UTR interaction is absent on non-polyadenylated histone mRNAs, which are not typically subjected to the same quality control mechanisms as polyadenylated mRNAs. Lack of Interaction with Quality Control Factors: The study did not identify interactions between eIF3 and known quality control factors, although this does not rule out the possibility of transient or indirect interactions. Further experiments are needed to definitively distinguish between these possibilities. Investigating eIF3's interaction with 3'-UTRs under conditions specifically inducing ribosome stalling or activating quality control pathways would provide valuable insights.

Core Concepts

eIF3, a key translation initiation factor, interacts with 3'-UTR termini of actively translated mRNAs in neural progenitor cells, suggesting a role in mRNA circularization and challenging the traditional understanding of its function.

Abstract

Bibliographic Information: Not applicable (content provided is an abstract and introduction section, not a full research paper).
Research Objective: This study investigates the role of eukaryotic initiation factor 3 (eIF3) in the global increase in protein synthesis observed during the early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs).
Methodology: The researchers employed several techniques, including Quick-irCLIP to identify RNA transcripts interacting with eIF3, APA-Seq to map polyadenylation events, and ribosome profiling to analyze translation activity in undifferentiated and differentiated NPCs.
Key Findings:
- eIF3 predominantly crosslinks with 3’-UTR termini of multiple mRNA isoforms, adjacent to the poly(A) tail.
- eIF3 engagement at 3’-UTR ends is dependent on polyadenylation but independent of direct interactions with poly(A)-binding proteins.
- High eIF3 crosslinking at 3’-UTR termini correlates with high translational activity, as determined by ribosome profiling.
Main Conclusions: The findings suggest that eIF3 plays a role in mRNA circularization, potentially facilitating communication between the 5’ and 3’ ends of actively translated mRNAs. This challenges the traditional view of eIF3's role solely in translation initiation and points to a more complex regulatory function.
Significance: This research provides novel insights into the mechanisms governing mRNA translation and the role of eIF3 in this process, particularly in the context of stem cell differentiation and the accompanying translational burst.
Limitations and Future Research: The study primarily focuses on early NPC differentiation. Further research is needed to explore the role of eIF3 in mRNA circularization in other cell types and differentiation stages. Additionally, identifying the specific proteins interacting with eIF3 at the 3’-UTR termini and elucidating the detailed molecular mechanisms underlying this interaction will be crucial for a comprehensive understanding of this novel function.

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Stats

NPCs treated with forebrain neuron differentiation medium for 2 hours show a significant increase in puromycin incorporation into nascent chains compared to undifferentiated NPCs, indicating a differentiation-dependent global increase in protein synthesis.
eIF3 predominantly (>90%) crosslinks to mRNAs over other non-coding RNAs.
In both differentiated and undifferentiated NPCs, 58% and 55% of the 3’-UTR eIF3 crosslinks, respectively, map to regions enriched in the canonical PAS sequence AAUAAA.
Ribosome profiling reveals that for approximately 75% of mRNAs, translation efficiency levels remain unchanged upon NPC differentiation.
ID2 mRNA shows a >5-fold increase in RPF count upon NPC differentiation, indicating a significant burst in translation activity.

Quotes

Key Insights Distilled From

eIF3 engages with 3’-UTR termini of highly translated mRNAs

by Mestre-Fos,S... at www.biorxiv.org 11-11-2023

https://www.biorxiv.org/content/10.1101/2023.11.11.566681v3

Deeper Inquiries

How does the role of eIF3 in mRNA circularization differ across various cell types and differentiation stages beyond early NPCs?

While the study focuses on early NPCs, the role of eIF3 in mRNA circularization likely exhibits cell type- and differentiation stage-specific variations. Here's why:

Translational Landscape: Different cell types and differentiation stages possess unique translational landscapes, influenced by factors like transcription factor availability, RNA-binding protein expression, and signaling pathways. These factors can alter the repertoire of actively translated mRNAs, potentially impacting eIF3's 3'-UTR engagement and its role in circularization.
eIF3 Subunit Composition:  The eIF3 complex comprises 13 subunits, some of which exhibit tissue-specific expression and post-translational modifications. Variations in eIF3 subunit composition could influence its interactions with RNA and other proteins, potentially affecting its role in mRNA circularization in a cell type- and differentiation stage-dependent manner.
Alternative Polyadenylation (APA): APA, a process generating mRNA isoforms with different 3'-UTR lengths, is highly regulated during development and differentiation. Since eIF3 interacts with 3'-UTR termini, variations in APA patterns across cell types and differentiation stages could influence eIF3's binding sites and its role in circularization.
Crosstalk with Other Regulatory Mechanisms: mRNA circularization is a dynamic process influenced by multiple factors, including RNA modifications (e.g., m6A), RNA-binding proteins, and microRNAs. The interplay between these factors and eIF3's role in circularization likely varies across cell types and differentiation stages.
Further research is needed to elucidate the precise mechanisms underlying these potential variations and their functional implications. Investigating eIF3's role in mRNA circularization across a broader range of cell types and differentiation stages will provide a more comprehensive understanding of its contribution to translational regulation.

Could the observed eIF3 interaction with 3'-UTR termini be a consequence of ribosome stalling or quality control mechanisms rather than active translation?

While the study suggests a correlation between eIF3's 3'-UTR interaction and active translation, the possibility of ribosome stalling or quality control mechanisms contributing to this observation cannot be entirely ruled out. Here's why:

Ribosome Stalling: Stalled ribosomes can trigger mRNA quality control pathways, potentially leading to the recruitment of eIF3 to the 3'-UTR. This recruitment could be part of a surveillance mechanism to assess the stalled ribosome or facilitate its rescue or disassembly.
Nonsense-Mediated Decay (NMD): NMD is a quality control pathway targeting mRNAs with premature termination codons (PTCs). Ribosome stalling at PTCs can trigger NMD, and eIF3's presence at the 3'-UTR could be linked to this process.
No-Go Decay (NGD): NGD targets mRNAs with strong stalls in the coding sequence. Similar to NMD, eIF3's 3'-UTR interaction could be associated with NGD-mediated mRNA degradation.
However, several observations in the study argue against these possibilities:

Correlation with Translation Levels: The study demonstrates a positive correlation between eIF3's 3'-UTR binding and ribosome occupancy, suggesting a link to active translation rather than solely stalling or quality control.
Absence on Non-polyadenylated mRNAs: eIF3's 3'-UTR interaction is absent on non-polyadenylated histone mRNAs, which are not typically subjected to the same quality control mechanisms as polyadenylated mRNAs.
Lack of Interaction with Quality Control Factors: The study did not identify interactions between eIF3 and known quality control factors, although this does not rule out the possibility of transient or indirect interactions.
Further experiments are needed to definitively distinguish between these possibilities. Investigating eIF3's interaction with 3'-UTRs under conditions specifically inducing ribosome stalling or activating quality control pathways would provide valuable insights.

If eIF3 is indeed involved in mRNA circularization, what implications might this have for the development of translation-targeted therapies?

If eIF3's role in mRNA circularization is confirmed and found to be essential for regulating translation, it could open up new avenues for developing translation-targeted therapies. Here are some potential implications:

Targeting eIF3-mRNA Interactions: Developing small molecules or RNA-based therapeutics that specifically disrupt or enhance eIF3's interaction with 3'-UTR termini could modulate translation of target mRNAs. This approach could be particularly relevant for diseases caused by the overexpression or underexpression of specific proteins.
Manipulating mRNA Circularization: Targeting the factors involved in mRNA circularization, including eIF3 and its interacting partners, could provide a means to globally tune translation. This approach could be beneficial for conditions characterized by dysregulated global translation, such as cancer.
Enhancing mRNA Vaccines and Therapeutics: mRNA-based vaccines and therapeutics rely on efficient translation of the delivered mRNA. Understanding eIF3's role in mRNA circularization could lead to strategies for optimizing mRNA design and delivery to enhance translation efficiency and therapeutic efficacy.
Developing Novel Biomarkers:  Altered eIF3 expression or activity, as well as disruptions in mRNA circularization, could serve as potential biomarkers for diseases characterized by dysregulated translation. Monitoring these biomarkers could aid in disease diagnosis, prognosis, and treatment response prediction.
However, several challenges need to be addressed before translating these implications into therapeutic applications:

Specificity:  Developing therapeutics that specifically target eIF3's role in mRNA circularization without affecting its other essential functions in translation initiation will be crucial to minimize off-target effects.
Delivery: Efficient delivery of therapeutics to the target cells and tissues will be essential for achieving therapeutic efficacy.
Safety:  Thorough preclinical and clinical studies will be necessary to assess the safety and efficacy of any translation-targeted therapies.
Despite these challenges, understanding eIF3's role in mRNA circularization holds significant promise for developing novel therapeutic strategies for a wide range of diseases. Further research in this area is warranted to unlock the full therapeutic potential of targeting this fundamental cellular process.