The separation between the 5′-3′ ends in long RNA molecules is short and nearly constant

Leija-Martínez, Nehemías; Casas-Flores, Sergio; Cadena-Nava, Rubén D.; Roca, Joan A.; Mendez, José Alfredo; Gomez, E.; Ruíz-García, Jaime

doi:10.1093/nar/gku1249

Cited by 31 publications

(33 citation statements)

References 43 publications

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“…These sequences were folded in vitro without any protein factors, and single-molecule Förster resonance energy transfer (smFRET) was observed between the two ends of the molecules. When FRET was detected, the end-to-end distance ranged from 5 to 9 nanometers (Leija-Martinez et al, 2014). These results are consistent with the computational studies suggesting that the 5' and 3' ends in all RNAs are invariably close and tend to basepair to each other.…”

Section: Rna Has the Intrinsic Propensity To Fold Into Structures Thatsupporting

confidence: 88%

“…These computational predictions were first tested using several viral RNAs and mRNAs from the fungus Trichoderma atroviride with lengths from 500 to 5,000 nucleotides (Leija-Martinez et al, 2014). These sequences were folded in vitro without any protein factors, and single-molecule Förster resonance energy transfer (smFRET) was observed between the two ends of the molecules.…”

Section: Rna Has the Intrinsic Propensity To Fold Into Structures Thatmentioning

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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Section: Rna Has the Intrinsic Propensity To Fold Into Structures Thatsupporting

confidence: 88%

Section: Rna Has the Intrinsic Propensity To Fold Into Structures Thatmentioning

confidence: 99%

Making ends meet: new functions of mRNA secondary structure

Ermolenko

Mathews

2020

Preprint

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“…Some observations suggest that the inherent folding of RNA may contribute to the formation of the "closed-loop" nature of mRNPs. For example, the ends of purified mRNAs folded in vitro are close (<10 nm) in solution (Fang et al 2011;Yoffe et al 2011;Clote et al 2012;Leija-Martínez et al 2014;Lai et al 2018). This distance is significantly smaller than the overall size of the mRNA when compacted.…”

Section: Nontranslating Mrnas Form Compacted Structuresmentioning

confidence: 99%

The landscape of eukaryotic mRNPs

Khong

Parker

2019

RNA

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The proper regulation of mRNA processing, localization, translation, and degradation occurs on mRNPs. However, the global principles of mRNP organization are poorly understood. We utilize the limited, but existing, information available to present a speculative synthesis of mRNP organization with the following key points. First, mRNPs form a compacted structure due to the inherent folding of RNA. Second, the ribosome is the principal mechanism by which mRNA regions are partially decompacted. Third, mRNPs are 50%-80% protein by weight, consistent with proteins modulating mRNP organization, but also suggesting the majority of mRNA sequences are not directly interacting with RNA-binding proteins. Finally, the ratio of mRNA-binding proteins to mRNAs is higher in the nucleus to allow effective RNA processing and limit the potential for nuclear RNA based aggregation. This synthesis of mRNP understanding provides a model for mRNP biogenesis, structure, and regulation with multiple implications.

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“…However, it is known that the mRNA from the meta pathway is quite short lived and starts being degraded before it is fully synthesized (32). Note also that mRNA tends to form secondary structures that shorten the distances between the 5′ and 3′ ends (33). On this basis, we argue that separation of red and green spots in the images shown in Fig.…”

Section: Resultsmentioning

confidence: 69%

The subcellular architecture of thexylgene expression flow of the TOL catabolic plasmid ofPseudomonas putidamt-2

Kim

Goñi-Moreno

2020

Preprint

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Despite intensive research on the biochemical and regulatory features of the archetypal catabolic TOL system borne by pWW0 of Pseudomonas putida mt-2, the physical arrangement and tridimensional logic of the xyl gene expression flow remains unknown. In this work, the spatial distribution of specific xyl mRNAs with respect to the host nucleoid, the TOL plasmid and the ribosomal pool has been investigated. In situ hybridization of target transcripts with fluorescent oligonucleotide probes revealed that xyl mRNAs cluster in discrete foci, adjacent but clearly separated from the TOL plasmid and the cell nucleoid. Also, they co-localize with ribosome-rich domains of the intracellular milieu. This arrangement was kept even when the xyl genes were artificially relocated at different chromosomal locations. The same happened when genes were expressed through a heterologous T7 polymerase-based system, which originated mRNA foci outside the DNA. In contrast, rifampicin treatment, known to ease crowding, blurred the confinement of xyl transcripts. This suggested that xyl mRNAs intrinsically run away from their initiation sites to ribosome-rich points for translation—rather than being translated coupled to transcription. Moreover, the results suggest that the distinct subcellular motion of xyl mRNAs results both from innate properties of the sequence at stake and the physical forces that keep the ribosomal pool away from the nucleoid in P. putida. This scenario is discussed on the background of current knowledge on the 3D organization of the gene expression flow in other bacteria and the environmental lifestyle of this soil microorganism.IMPORTANCEThe transfer of information between DNA, RNA and proteins in a bacterium is often compared to the decoding of a piece of software in a computer. However, the tridimensional layout and the relational logic of the cognate biological hardware i.e. the nucleoid, the RNA polymerase and the ribosomes, are habitually taken for granted. In this work we inspected the localization and fate of the transcripts that stem from the archetypal biodegradative plasmid pWW0 of soil bacterium Pseudomonas putida KT2440 through the non-homogenous milieu of the bacterial cytoplasm. The results expose that—similarly to computers also—the material components that enable the expression flow are well separated physically and they decipher the sequences through a distinct tridimensional arrangement with no indication of transcription/translation coupling. We argue that the resulting subcellular architecture enters an extra regulatory layer that obeys a species-specific positional code that accompanies the environmental lifestyle of this bacterium.

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The separation between the 5′-3′ ends in long RNA molecules is short and nearly constant

Cited by 31 publications

References 43 publications

Making ends meet: new functions of mRNA secondary structure

Making ends meet: new functions of mRNA secondary structure

The landscape of eukaryotic mRNPs

The subcellular architecture of thexylgene expression flow of the TOL catabolic plasmid ofPseudomonas putidamt-2

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