Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. [PDF]
Noncoding RNA, 2021 Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation.
Skeparnias I, Zhang J.
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Protocol to assess RNA-RNA interactions in situ using an RNA-proximity ligation assay. [PDF]
STAR Protoc, 2022 Summary: Here, we describe a protocol to assess RNA-RNA interactions in situ using an adapted proximity ligation assay (PLA). We detail steps to perform RNA-probe hybridization, in situ rolling circle amplification, and immunofluorescence confocal ...
Basavappa MG, Henao-Mejia J, Cherry S.
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lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK. [PDF]
PLoS Genet, 2023 RNA-RNA interactions play a crucial role in regulating gene expression and various biological processes, but identifying these interactions on a transcriptomic scale remains a challenge.
Hu Y +9 more
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Simultaneous Capture of Chromatin-Associated RNA and Global RNA-RNA Interactions With Reduced Input Requirements. [PDF]
Bio ProtocChromatin-associated RNAs (caRNAs) have been increasingly recognized as key regulators of gene expression and genome architecture. A few technologies, such as ChRD-PET and RedChIP, have emerged to assess protein-mediated RNA–chromatin interactions, but ...
Ding C +10 more
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Long-distance RNA–RNA interactions shape dynamic RNA architectures and functional states in plant positive-strand RNA viruses [PDF]
Front MicrobiolThe genomes of positive-strand RNA [(+)ssRNA] viruses function as dynamic RNA molecules that participate in multiple, sometimes competing, processes during infection, including translation, genome replication, subgenomic RNA (sgRNA) transcription, and ...
Wang D, Wu H, Zhang X, Chang Q, Yuan X.
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Trans-Acting RNA-RNA Interactions in Segmented RNA Viruses. [PDF]
Viruses, 2019 RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single ...
Newburn LR, White KA.
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Intragenomic Long-Distance RNA-RNA Interactions in Plus-Strand RNA Plant Viruses. [PDF]
Front Microbiol, 2018 Plant viruses that contain positive-strand RNA genomes represent an important class of pathogen. The genomes of these viruses harbor RNA sequences and higher-order RNA structures that are essential for the regulation of viral processes during infections.
Chkuaseli T, White KA.
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High-Resolution Mapping of RNA-RNA Interactions Across the HIV-1 Genome With HicapR. [PDF]
Bio ProtocThe genomes of RNA viruses can fold into dynamic structures that regulate their own infection and immune evasion processes. Proximity ligation methods (e.g., SPLASH) enable genome-wide interaction mapping but lack specificity when dealing with low ...
Wang H +10 more
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Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network. [PDF]
Cell Rep, 2020 Summary: Selective assembly of influenza virus segments into virions is proposed to be mediated through intersegmental RNA-RNA interactions. Here, we developed a method called 2CIMPL that includes proximity ligation under native conditions to identify ...
Le Sage V +5 more
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Protocol for profiling virus-to-host RNA-RNA interactions in infected cells by RIC-seq. [PDF]
STAR ProtocSummary: Virus-to-host RNA-RNA interactions directly regulate host mRNA stability and viral replication. However, globally profiling virus-to-host in situ RNA-RNA interactions remains challenging.
Cai Z, Zhao H, Xue Y.
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