The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

Horváthová, Ivana; Voigt, Franka; Kotrys, Anna V.; Zhan, Yinxiu; Artus‐Revel, Caroline G; Eglinger, Jan; Stadler, Michael; Giorgetti, Luca; Chao, Jeffrey A.

doi:10.1016/j.molcel.2017.09.030

Cited by 184 publications

(167 citation statements)

References 68 publications

(67 reference statements)

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“…We recently identified the transcriptome and proteome of PBs purified from human cells. Their analysis showed that human PBs are broadly involved in mRNA storage rather than decay [2,3], as also observed using fluorescent decay reporters [4]. However, the mechanism underlying the large but specific targeting of mRNAs to PBs is still unknown, though it clearly results in the co-recruitment of particular RBPs [2].…”

Section: Introductionmentioning

confidence: 79%

GC content shapes mRNA decay and storage in human cells

Courel

Clément

Foretek

et al. 2018

Preprint

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Control of protein expression results from the fine tuning of mRNA synthesis, decay and translation. These processes, which are controlled by a large number of RNA-binding proteins and by localization in RNP granules such as P-bodies, appear often intimately linked although the rules of this interplay are not well understood. In this study, we combined our recent P-body transcriptome with various transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors. This analysis revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA decay. It also rationalized why PBs mRNAs have a strikingly low protein yield. We report too the existence of distinct mRNA decay pathways with preference for AU-rich or GC-rich transcripts. Compared to this impact of the GC content, sequence-specific RBPs and miRNAs appeared to have only modest additional effects on their bulk targets. Altogether, these results lead to an integrated view of post-transcriptional control in human cells where most regulation at the level of translation is dedicated to AU-rich mRNAs, which have a limiting protein yield, whereas regulation at the level of 5' decay applies to GC-rich mRNAs, whose translation is optimal.

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Section: Introductionmentioning

confidence: 79%

GC content shapes mRNA decay and storage in human cells

Courel

Clément

Foretek

et al. 2018

Preprint

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“…The MS2-MCP system has been used in conjunction with other binary systems like the ones provided by PP7 stem-loops and PP7 protein to visualize transcripts undergoing pioneering round of translation (Halstead et al, 2015) or to study the dynamics of mRNA turnover (Horvathova et al, 2017). These methods however do not allow high temporal resolution of mRNA translation due to the time needed for the synthesis of the fluorescent protein.…”

Section: New Technologies To Study Mrna Expression In Neuronsmentioning

confidence: 99%

Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity

Andreassi

Crerar

Riccio

2018

Front. Mol. Neurosci.

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Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their extraordinary cytoarchitecture. This formidable task is achieved, at least in part, by targeting mRNA to subcellular compartments where they are rapidly translated. mRNA transcripts are the conveyor of genetic information from DNA to the translational machinery, however, they are also endowed with additional functions linked to both the coding sequence (open reading frame, or ORF) and the flanking 5′ and 3′ untranslated regions (UTRs), that may harbor coding-independent functions. In this review, we will highlight recent evidences supporting new coding-dependent and -independent functions of mRNA and discuss how nuclear and cytoplasmic post-transcriptional modifications of mRNA contribute to localization and translation in mammalian cells with specific emphasis on neurons. We also describe recently developed techniques that can be employed to study RNA dynamics at subcellular level in eukaryotic cells in developing and regenerating neurons.

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“…Therefore, actively-translating mRNAs generate two fluorescence signals, whereas untranslated mRNAs only generate an RFP signal. In addition to reporters of translation, a biosensor called TREAT (3’-RNA end accumulation during turnover) has been developed to track mRNA turnover in eukaryotes ((126, 141)). In this approach, the 3’UTR is engineered to include two viral pseudoknots (PKs) flanked by PP7 and MS2 binding sites (Figure 3E).…”

Section: Emerging Strategies and Approachesmentioning

confidence: 99%

“…Such physical magnification leads to an enhanced effective spatial resolution (126, 141). Recently, expansion microscopy has been combined with FISH imaging of RNA (144) in addition to immunofluorescence, and iterative expansion microscopy further enhances resolution from ~70 nm to ~25 nm (145).…”

Section: Emerging Strategies and Approachesmentioning

confidence: 99%

RNA Localization in Bacteria

Fei

Sharma

2018

Microbiol Spectr

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Diverse mechanisms and functions of post-transcriptional regulation by small regulatory RNAs (sRNAs) and RNA binding proteins (RBPs) have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due the small size of bacterial cells, localized RNA and translation are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or independent processes. We also provide an overview of the state-of-the-art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to in vivo imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.

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The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

Cited by 184 publications

References 68 publications

GC content shapes mRNA decay and storage in human cells

GC content shapes mRNA decay and storage in human cells

Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity

RNA Localization in Bacteria

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