A small stem-loop-forming region within the 3′-UTR of a nonpolyadenylated LCMV mRNA promotes translation

Hashizume, Mei; Takashima, Ayako; Iwasaki, Masaharu

doi:10.1016/j.jbc.2022.101576

Cited by 7 publications

(6 citation statements)

References 42 publications

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“…Second, we analyzed the host transcriptome in response to mammalian orthoreovirus infection. Members of the Reoviridae family of viruses synthesize nonpolyadenylated viral mRNAs, as do arenaviruses and flaviviruses [36][37][38] . Because STRS can directly capture viral RNAs, we could directly compare viral RNA abundance with gene expression changes in heart tissue.…”

Section: Discussionmentioning

confidence: 99%

Spatial mapping of the total transcriptome by in situ polyadenylation

et al. 2022

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Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNA enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We demonstrate that our spatial total RNA-sequencing (STRS) approach captures coding RNAs, noncoding RNAs and viral RNAs. We apply STRS to study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify spatially defined expression of noncoding transcripts in skeletal muscle regeneration and highlight host transcriptional responses associated with local viral RNA abundance. STRS requires adding only one step to the widely used Visium spatial total RNA-sequencing protocol from 10x Genomics, and thus could be easily adopted to enable new insights into spatial gene regulation and biology.

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Section: Discussionmentioning

confidence: 99%

Spatial mapping of the total transcriptome by in situ polyadenylation

et al. 2022

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“…Second, we analyzed the host transcriptome in response to mammalian orthoreovirus infection. Members of the Reoviridae family of viruses synthesize non-polyadenylated viral mRNAs as do Arenaviruses, and flaviviruses [33][34][35] . Because STRS can directly capture viral RNAs, we could directly compare viral RNA abundance to gene expression changes in heart tissue.…”

Section: Discussionmentioning

confidence: 99%

In situ polyadenylation enables spatial mapping of the total transcriptome

McKellar

Mantri

Hinchman

et al. 2022

Preprint

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Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNA enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We apply this Spatial Total RNA-Sequencing (STRS) approach to study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify spatially defined expression of noncoding transcripts in skeletal muscle regeneration, and highlight host transcriptional responses associated with local viral RNA abundance. In situ polyadenylation requires the addition of only a single step to a widely used protocol for spatial RNA-sequencing, and thus could be broadly and quickly adopted. Spatial RNA-sequencing of the total transcriptome will enable new insights into spatial gene regulation and biology.

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“…Viruses have highly diverse RNA structures; this diversity partially arises from the evolutionary pressure to constrain genome length [ 28 ]. This limitation has promoted the adaptation of RNA structure for a diverse set of alternative functions, spanning from orchestrating virion assembly to modulating viral protein levels [ 29 , 30 ]. This makes an in-depth understanding of RNA structural dynamics important for the development of antiviral compounds, given the pivotal role played by RNA structures in the interplay of viral life cycles and their multifunctional roles.…”

Section: Optical Tweezers For Studying Rna Structurementioning

confidence: 99%

The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA

Marinus,

Foster,

Tych

2024

Biochemical Society Transactions

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RNA, a dynamic and flexible molecule with intricate three-dimensional structures, has myriad functions in disease development. Traditional methods, such as X-ray crystallography and nuclear magnetic resonance, face limitations in capturing real-time, single-molecule dynamics crucial for understanding RNA function. This review explores the transformative potential of single-molecule force spectroscopy using optical tweezers, showcasing its capability to directly probe time-dependent structural rearrangements of individual RNA molecules. Optical tweezers offer versatility in exploring diverse conditions, with the potential to provide insights into how environmental changes, ligands and RNA-binding proteins impact RNA behaviour. By enabling real-time observations of large-scale structural dynamics, optical tweezers emerge as an invaluable tool for advancing our comprehension of RNA structure and function. Here, we showcase their application in elucidating the dynamics of RNA elements in virology, such as the pseudoknot governing ribosomal frameshifting in SARS-CoV-2.

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A small stem-loop-forming region within the 3′-UTR of a nonpolyadenylated LCMV mRNA promotes translation

Cited by 7 publications

References 42 publications

Spatial mapping of the total transcriptome by in situ polyadenylation

Spatial mapping of the total transcriptome by in situ polyadenylation

In situ polyadenylation enables spatial mapping of the total transcriptome

The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA

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