Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway

Adivarahan, Srivathsan; Livingston, Nathan M.; Nicholson, Beth; Rahman, Shadab A.; Wu, Bin; Rissland, Olivia S.; Zenklusen, Daniel

doi:10.1016/j.molcel.2018.10.010

Cited by 122 publications

(205 citation statements)

References 76 publications

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“…However, the versatility of the mRNA circularization has been challenged recently by the indications that the closed-loop conformation is rarely observed in living mammalian cells under normal conditions [69,70], that the predominant form of actively translated mRNA is likely not circularized in yeast and mammals [16,71], and that the polysome topology in a plant cell-free system undergoes complicated step-wise evolution accompanied by translation efficiency changes [72,73]. On the other hand, new evidence of functional mRNA cyclization came from recent studies of m 6 A mRNA methylation that brings 5 and 3 UTRs together via eIF3h-METTL3 interaction and/or cap/eIF4F/eIF3/YTHDF1/m6A bridge formation, which facilitates translation during oncogenesis [28,29].…”

Section: Discussionmentioning

confidence: 99%

Functional Cyclization of Eukaryotic mRNAs

Alekhina

Terenin

Dmitriev

et al. 2020

IJMS

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The closed-loop model of eukaryotic translation states that mRNA is circularized by a chain of the cap-eIF4E-eIF4G-poly(A)-binding protein (PABP)-poly(A) interactions that brings 5 and 3 ends together. This circularization is thought to promote the engagement of terminating ribosomes to a new round of translation at the same mRNA molecule, thus enhancing protein synthesis. Despite the general acceptance and the elegance of the hypothesis, it has never been proved experimentally. Using continuous in situ monitoring of luciferase synthesis in a mammalian in vitro system, we show here that the rate of translation initiation at capped and polyadenylated reporter mRNAs increases after the time required for the first ribosomes to complete mRNA translation. Such acceleration strictly requires the presence of a poly(A)-tail and is abrogated by the addition of poly(A) RNA fragments or m 7 GpppG cap analog to the translation reaction. The optimal functional interaction of mRNA termini requires 5 untranslated region (UTR) and 3 UTR of moderate lengths and provides stronger acceleration, thus a longer poly(A)-tail. Besides, we revealed that the inhibitory effect of the dominant negative R362Q mutant of initiation factor eIF4A diminishes in the course of translation reaction, suggesting a relaxed requirement for ATP. Taken together, our results imply that, upon the functional looping of an mRNA, the recycled ribosomes can be recruited to the start codon of the same mRNA molecule in an eIF4A-independent fashion. This non-canonical closed-loop assisted reinitiation (CLAR) mode provides efficient translation of the functionally circularized mRNAs.

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Section: Discussionmentioning

confidence: 99%

Functional Cyclization of Eukaryotic mRNAs

Alekhina

Terenin

Dmitriev

et al. 2020

IJMS

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“…Another line of evidence comes from single-molecule-resolution fluorescent in situ hybridization (smFISH) imaging studies in human cells. The median distance between the 5' and 3' ends of actively translated mRNAs, with lengths from 6,000 to 18,000 nucleotides, was 100-200 nm (Adivarahan et al, 2018;Khong & Parker, 2018). By contrast, the 5' and 3' ends in these mRNAs co-localized when translation was inhibited with arsenite or the antibiotic puromycin (Adivarahan et al, 2018;Khong & Parker, 2018).…”

Section: Mrna Compactness and The Closed-loop Model Of Translation Inmentioning

confidence: 95%

“…By contrast, the 5' and 3' ends in these mRNAs co-localized when translation was inhibited with arsenite or the antibiotic puromycin (Adivarahan et al, 2018;Khong & Parker, 2018). Strikingly, the colocalization of mRNA ends was observed in cells in which the eIF4G•PABP interaction was disrupted by mutagenesis (Adivarahan et al, 2018). Based on these experiments, it was concluded that, in the absence of helicase activity of translating ribosomes, mRNA ends come in close proximity because of intramolecular basepairing interactions within mRNA (Adivarahan et al, 2018;Khong & Parker, 2018).…”

Section: Mrna Compactness and The Closed-loop Model Of Translation Inmentioning

confidence: 97%

“…The median distance between the 5' and 3' ends of actively translated mRNAs, with lengths from 6,000 to 18,000 nucleotides, was 100-200 nm (Adivarahan et al, 2018;Khong & Parker, 2018). By contrast, the 5' and 3' ends in these mRNAs co-localized when translation was inhibited with arsenite or the antibiotic puromycin (Adivarahan et al, 2018;Khong & Parker, 2018). Strikingly, the colocalization of mRNA ends was observed in cells in which the eIF4G•PABP interaction was disrupted by mutagenesis (Adivarahan et al, 2018).…”

Section: Mrna Compactness and The Closed-loop Model Of Translation Inmentioning

confidence: 97%

“…Strikingly, the colocalization of mRNA ends was observed in cells in which the eIF4G•PABP interaction was disrupted by mutagenesis (Adivarahan et al, 2018). Based on these experiments, it was concluded that, in the absence of helicase activity of translating ribosomes, mRNA ends come in close proximity because of intramolecular basepairing interactions within mRNA (Adivarahan et al, 2018;Khong & Parker, 2018). Hence, at least in the translationally repressed state of mRNA, for example, in mRNAs sequestered into stress granules (Adivarahan et al, 2018;Khong & Parker, 2018), mRNA ends are brought in close proximity by mRNA secondary structure.…”

Section: Mrna Compactness and The Closed-loop Model Of Translation Inmentioning

confidence: 99%

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Making ends meet: new functions of mRNA secondary structure

Ermolenko

Mathews

2020

Preprint

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The 5' cap and 3' poly(A) tail of mRNA are known to synergistically regulate mRNA translation and stability. Recent computational and experimental studies revealed that both protein-coding and non-coding RNAs will fold with extensive intramolecular secondary structure, which will result in close distances between the sequence ends. This proximity of the ends is a sequence-independent, universal property of most RNAs. Only low-complexity sequences without guanosines are without secondary structure and exhibit end-to-end distances expected for RNA random coils. The innate proximity of RNA ends might have important biological implications that remain unexplored. In particular, the inherent compactness of mRNA might regulate translation initiation by facilitating the formation of protein complexes that bridge mRNA 5' and 3' ends. Additionally, the proximity of mRNA ends might mediate coupling of 3′ deadenylation to 5′ end mRNA decay.

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The separation between mRNA‐ends is more variable than expected

Gerling,

Mendez,

Gomez

et al. 2024

FEBS Open Bio

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Effective circularization of mRNA molecules is a key step for the efficient initiation of translation. Research has shown that the intrinsic separation of the ends of mRNA molecules is rather small, suggesting that intramolecular arrangements could provide this effective circularization. Considering that the innate proximity of RNA ends might have important unknown biological implications, we aimed to determine whether the close proximity of the ends of mRNA molecules is a conserved feature across organisms and gain further insights into the functional effects of the proximity of RNA ends. To do so, we studied the secondary structure of 274 full native mRNA molecules from 17 different organisms to calculate the contour length (CL) of the external loop as an index of their end‐to‐end separation. Our computational predictions show bigger variations (from 0.59 to 31.8 nm) than previously reported and also than those observed in random sequences. Our results suggest that separations larger than 18.5 nm are not favored, whereas short separations could be related to phenotypical stability. Overall, our work implies the existence of a biological mechanism responsible for the increase in the observed variability, suggesting that the CL features of the exterior loop could be relevant for the initiation of translation and that a short CL could contribute to the stability of phenotypes.

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Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway

Cited by 122 publications

References 76 publications

Functional Cyclization of Eukaryotic mRNAs

Functional Cyclization of Eukaryotic mRNAs

Making ends meet: new functions of mRNA secondary structure

The separation between mRNA‐ends is more variable than expected

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