scholarly journals The short- and long-range RNA-RNA Interactome of SARS-CoV-2

2020 ◽  
Author(s):  
Omer Ziv ◽  
Jonathan Price ◽  
Lyudmila Shalamova ◽  
Tsveta Kamenova ◽  
Ian Goodfellow ◽  
...  
Keyword(s):  
Long Range ◽  
Rna Structure ◽  
Purifying Selection ◽  
Etiologic Agent ◽  
Long Distance ◽  
Rna Interaction ◽  
Positive Strand Rna ◽  
Discontinuous Transcription ◽  
Transcription And Replication

SUMMARYThe Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies.

scholarly journals In vivo structure and dynamics of the RNA genome of SARS-Cov-2

2021 ◽  
Author(s):  
Yan Zhang ◽  
Kun Huang ◽  
Dejian Xie ◽  
Jian You Lau ◽  
Wenlong Shen ◽  
...  
Keyword(s):  
Life Cycle ◽  
Structural Basis ◽  
Rna Structures ◽  
Long Distance ◽  
Alternative Structures ◽  
Translational Frameshifting ◽  
Ribosome Stalling ◽  
Positive Strand Rna ◽  
Discontinuous Transcription

AbstractThe SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3’-UTR and 5’-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a “high-order pseudoknot” embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

scholarly journals In vivo structure and dynamics of the SARS-CoV-2 RNA genome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yan Zhang ◽  
Kun Huang ◽  
Dejian Xie ◽  
Jian You Lau ◽  
Wenlong Shen ◽  
...  
Keyword(s):  
Life Cycle ◽  
Rna Structure ◽  
Structural Basis ◽  
Long Distance ◽  
Alternative Structures ◽  
Translational Frameshifting ◽  
Functional Relevance ◽  
Discontinuous Transcription ◽  
Whole Life Cycle

AbstractThe dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5′-UTR and 3′-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

scholarly journals Mechanism of Stimulation of Plus-Strand Synthesis by an RNA Replication Enhancer in a Tombusvirus

2005 ◽  
Vol 79 (15) ◽  
pp. 9777-9785 ◽  
Author(s):  
Tadas Panavas ◽  
Peter D. Nagy
Keyword(s):  
Rna Synthesis ◽  
Rna Viruses ◽  
Rna Replication ◽  
Dual Function ◽  
Long Distance ◽  
Replication Assay ◽  
Rna Interaction ◽  
Stimulation Of

ABSTRACT Replication of RNA viruses is regulated by cis-acting RNA elements, including promoters, replication silencers, and replication enhancers (REN). To dissect the function of an REN element involved in plus-strand RNA synthesis, we developed an in vitro trans-replication assay for tombusviruses, which are small plus-strand RNA viruses. In this assay, two RNA strands were tethered together via short complementary regions with the REN present in the nontemplate RNA, whereas the promoter was located in the template RNA. We found that the template activity of the tombusvirus replicase preparation was stimulated in trans by the REN, suggesting that the REN is a functional enhancer when located in the vicinity of the promoter. In addition, this study revealed that the REN has dual function during RNA synthesis. (i) It binds to the viral replicase. (ii) It interacts with the core plus-strand initiation promoter via a long-distance RNA-RNA interaction, which leads to stimulation of initiation of plus-strand RNA synthesis by the replicase in vitro. We also observed that this RNA-RNA interaction increased the in vivo accumulation and competitiveness of defective interfering RNA, a model template. We propose that REN is important for asymmetrical viral RNA replication that leads to more abundant plus-strand RNA progeny than the minus-strand intermediate, a hallmark of replication of plus-strand RNA viruses.

scholarly journals Microvilli-derived Extracellular Vesicles Govern Morphogenesis in Drosophila wing epithelium

2020 ◽  
Author(s):  
Ilse Hurbain ◽  
Anne-Sophie Macé ◽  
Maryse Romao ◽  
Lucie Sengmanivong ◽  
Laurent Ruel ◽  
...  
Keyword(s):  
Long Range ◽  
Extracellular Vesicles ◽  
Cell Biology ◽  
Extracellular Vesicle ◽  
Wing Disc ◽  
Cellular Mechanisms ◽  
Long Distance ◽  
Drosophila Wing ◽  
And Function

ABSTRACTThe regulation and coordination of developmental processes involves the secretion of morphogens and membrane carriers, including extracellular vesicles, which facilitate their transport over long distance. The long-range activity of the Hedgehog morphogen is conveyed by extracellular vesicles. However, the site and the molecular basis of their biogenesis remains unknown. By combining fluorescence and electron microscopy combined with genetics and cell biology approaches, we investigated the origin and the cellular mechanisms underlying extracellular vesicle biogenesis, and their contribution to Drosophila wing disc development, exploiting Hedgehog as a long-range morphogen. We show that microvilli of Drosophila wing disc epithelium are the site of generation of small extracellular vesicles that transport Hedgehog across the tissue. This process requires the Prominin-like protein, whose activity, together with interacting cytoskeleton components and lipids, is critical for maintaining microvilli integrity and function in secretion. Our results provide the first evidence that microvilli-derived extracellular vesicles contribute to Hedgehog long-range signaling activity highlighting their physiological significance in tissue development in vivo.

scholarly journals A Multicomponent RNA-Based Control System Regulates Subgenomic mRNA Transcription in a Tombusvirus

2006 ◽  
Vol 81 (5) ◽  
pp. 2429-2439 ◽  
Author(s):  
Han-Xin Lin ◽  
Wei Xu ◽  
K. Andrew White
Keyword(s):  
Control System ◽  
Premature Termination ◽  
Virus Genome ◽  
Mrna Transcription ◽  
Long Distance ◽  
Structural Integration ◽  
Rna Elements ◽  
High Level ◽  
Positive Strand Rna

ABSTRACT During infections, positive-strand RNA tombusviruses transcribe two subgenomic (sg) mRNAs that allow for the expression of a subset of their genes. This process is thought to involve an unconventional mechanism involving the premature termination of the virally encoded RNA-dependent RNA polymerase while it is copying the virus genome. The 3′ truncated minus strands generated by termination are then used as templates for sg mRNA transcription. In addition to requiring an extensive network of long-distance RNA-RNA interactions (H.-X. Lin and K. A. White, EMBO J. 23:3365-3374, 2004), the transcription of tombusvirus sg mRNAs also involves several additional RNA structures. In vivo analysis of these diverse RNA elements revealed that they function at distinct steps in the process by facilitating the formation or stabilization of the long-distance interactions, modulating minus-strand template production, or promoting the initiation of sg mRNA transcription. All of the RNA elements characterized could be readily incorporated into a premature termination model for sg mRNA transcription. Overall, the analyses revealed a complex system that displays a high level of structural integration and functional coordination. This multicomponent RNA-based control system may serve as a useful paradigm for understanding related transcriptional processes in other positive-sense RNA viruses.

scholarly journals Opium Poppy Mosaic Virus Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3′ CITE

2021 ◽  
Vol 95 (9) ◽  
Author(s):  
Muhammad Ilyas ◽  
Zhiyou Du ◽  
Anne E. Simon
Keyword(s):  
Mosaic Virus ◽  
Structural Features ◽  
Opium Poppy ◽  
Luciferase Reporter ◽  
Long Distance ◽  
Subgenomic Rna ◽  
The Family ◽  
Rna Interaction ◽  
Independent Translation

ABSTRACT Opium poppy mosaic virus (OPMV) is a recently discovered umbravirus in the family Tombusviridae. OPMV has a plus-sense genomic RNA (gRNA) of 4,241 nucleotides (nt) from which replication protein p35 and p35 extension product p98, the RNA-dependent RNA polymerase (RdRp), are expressed. Movement proteins p27 (long distance) and p28 (cell to cell) are expressed from a 1,440-nt subgenomic RNA (sgRNA2). A highly conserved structure was identified just upstream from the sgRNA2 transcription start site in all umbraviruses, which includes a carmovirus consensus sequence, denoting generation by an RdRp-mediated mechanism. OPMV also has a second sgRNA of 1,554 nt (sgRNA1) that starts just downstream of a canonical exoribonuclease-resistant sequence (xrRNAD). sgRNA1 codes for a 30-kDa protein in vitro that is in frame with p28 and cannot be synthesized in other umbraviruses. Eliminating sgRNA1 or truncating the p30 open reading frame (ORF) without affecting p28 substantially reduced accumulation of OPMV gRNA, suggesting a functional role for the protein. The 652-nt 3′ untranslated region of OPMV contains two 3′ cap-independent translation enhancers (3′ CITEs), a T-shaped structure (TSS) near its 3′ end, and a Barley yellow dwarf virus-like translation element (BTE) in the central region. Only the BTE is functional in luciferase reporter constructs containing gRNA or sgRNA2 5′ sequences in vivo, which differs from how umbravirus 3′ CITEs were used in a previous study. Similarly to most 3′ CITEs, the OPMV BTE links to the 5′ end via a long-distance RNA-RNA interaction. Analysis of 14 BTEs revealed additional conserved sequences and structural features beyond the previously identified 17-nt conserved sequence. IMPORTANCE Opium poppy mosaic virus (OPMV) is an umbravirus in the family Tombusviridae. We determined that OPMV accumulates two similarly sized subgenomic RNAs (sgRNAs), with the smaller known to code for proteins expressed from overlapping open reading frames. The slightly larger sgRNA1 has a 5′ end just upstream from a previously predicted xrRNAD site, identifying this sgRNA as an unusually long product produced by exoribonuclease trimming. Although four umbraviruses have similar predicted xrRNAD sites, only sgRNA1 of OPMV can code for a protein that is an extension product of umbravirus ORF4. Inability to generate the sgRNA or translate this protein was associated with reduced gRNA accumulation in vivo. We also characterized the OPMV BTE structure, a 3′ cap-independent translation enhancer (3′ CITE). Comparisons of 13 BTEs with the OPMV BTE revealed additional stretches of sequence similarity beyond the 17-nt signature sequence, as well as conserved structural features not previously recognized in these 3′ CITEs.

scholarly journals RNA structure through multidimensional chemical mapping

2016 ◽  
Author(s):  
Siqi Tian ◽  
Rhiju Das
Keyword(s):  
Structure Determination ◽  
Rna Structure ◽  
De Novo ◽  
Compensatory Mutation ◽  
Chemical Mapping ◽  
Rna Molecules ◽  
Viral Genomes ◽  
Rna Interaction

The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed .OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to two hundred nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches, that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-crosslink-map expansion to overcome this and other current limitations to resolving the in vivo "RNA structurome".

scholarly journals Actin-dependent intranuclear repositioning of an active gene locus in vivo

2007 ◽  
Vol 179 (6) ◽  
pp. 1095-1103 ◽  
Author(s):  
Miroslav Dundr ◽  
Jason K. Ospina ◽  
Myong-Hee Sung ◽  
Sam John ◽  
Madhvi Upender ◽  
...  
Keyword(s):  
Long Range ◽  
Transcriptional Activation ◽  
Gene Locus ◽  
Experimental System ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Small Nuclear Rna ◽  
Long Distance ◽  
Limited Mobility

Although bulk chromatin is thought to have limited mobility within the interphase eukaryotic nucleus, directed long-distance chromosome movements are not unknown. Cajal bodies (CBs) are nuclear suborganelles that nonrandomly associate with small nuclear RNA (snRNA) and histone gene loci in human cells during interphase. However, the mechanism responsible for this association is uncertain. In this study, we present an experimental system to probe the dynamic interplay of CBs with a U2 snRNA target gene locus during transcriptional activation in living cells. Simultaneous four-dimensional tracking of CBs and U2 genes reveals that target loci are recruited toward relatively stably positioned CBs by long-range chromosomal motion. In the presence of a dominant-negative mutant of β-actin, the repositioning of activated U2 genes is markedly inhibited. This supports a model in which nuclear actin is required for these rapid, long-range chromosomal movements.

scholarly journals Evidence for a long-r ange RNA-RNA interaction between ORF8 and the downstream region of the Spike polybasic insertion of SARS-CoV-2

2021 ◽  
Author(s):  
Amirhossein Manzourolajdad ◽  
Filipe Pereira
Keyword(s):  
Long Range ◽  
Genomic Region ◽  
Synonymous Mutation ◽  
Genomic Rna ◽  
Base Pairing ◽  
Genomic Rnas ◽  
Close Proximity ◽  
Candidate Regions ◽  
Rna Interaction ◽  
Discontinuous Transcription

SARS-CoV-2 has affected people all over the world as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV responsible for the 2002-2003 SARS outbreak in Asia. Intense research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Similar to other betacoronaviruses, long-range RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into different viral proteins. An important difference between both viruses is a polybasic insertion in the Spike region of SARS-CoV-2, absent in SARS-CoV. Here we show that a 26-base-pair long-range RNA-RNA interaction occurs between the genomic region downstream of the Spike insertion and ORF8 in SARS-CoV-2. Predictions suggest that the corresponding ORF8 region forms the most energetically favorable interaction with that of Spike region from amongst all possible candidate regions within SARS-CoV-2 genomic RNA. We also found signs of sequence covariation in the predicted interaction using a large dataset with 27,592 full-length SARS-CoV-2 genomes. In particular, a synonymous mutation in ORF8 accommodated for base pairing with Spike [G23675 C28045U], and a non-synonymous mutation in Spike accommodated for base pairing with ORF8 [C23679U G28042] both of which were in close proximity of one another. The predicted interactions can potentially be related to regulation of sub-genomic RNA production rates.

scholarly journals Direct visualization of a native Wnt in vivo reveals that a long-range Wnt gradient forms by extracellular dispersal

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Ariel M Pani ◽  
Bob Goldstein
Keyword(s):  
Long Range ◽  
Direct Evidence ◽  
Signaling Proteins ◽  
Long Distance ◽  
Biologically Relevant ◽  
C Elegans ◽  
Neuroblast Migration ◽  
Evolutionarily Conserved ◽  
First Time

Wnts are evolutionarily conserved signaling proteins with essential roles in development and disease that have often been thought to spread between cells and signal at a distance. However, recent studies have challenged this model, and whether long-distance extracellular Wnt dispersal occurs and is biologically relevant is debated. Understanding fundamental aspects of Wnt dispersal has been limited by challenges with observing endogenous ligands in vivo, which has prevented directly testing hypotheses. Here, we have generated functional, fluorescently tagged alleles for a C. elegans Wnt homolog and for the first time visualized a native, long-range Wnt gradient in a living animal. Live imaging of Wnt along with source and responding cell membranes provided support for free, extracellular dispersal. By limiting Wnt transfer between cells, we confirmed that extracellular spreading shapes a long-range gradient and is critical for neuroblast migration. These results provide direct evidence that Wnts spread extracellularly to regulate aspects of long-range signaling.

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