Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions [PDF]
Non-Coding 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.
Ilias Skeparnias, Jinwei Zhang
doaj +2 more sources
Protocol to assess RNA-RNA interactions in situ using an RNA-proximity ligation assay [PDF]
STAR Protocols, 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 ...
Megha G. Basavappa +2 more
doaj +2 more sources
lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK. [PDF]
PLoS Genetics, 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.
Yuanlang Hu +9 more
doaj +2 more sources
Investigating RNA–RNA interactions through computational and biophysical analysis [PDF]
Nucleic Acids Research, 2022 Abstract Numerous viruses utilize essential long-range RNA–RNA genome interactions, specifically flaviviruses. Using Japanese encephalitis virus (JEV) as a model system, we computationally predicted and then biophysically validated and characterized its long-range RNA–RNA genomic interaction.
Mrozowich, Tyler +10 more
europepmc +6 more sources
Simultaneous Capture of Chromatin-Associated RNA and Global RNA–RNA Interactions With Reduced Input Requirements [PDF]
Bio-ProtocolChromatin-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 ...
Cheng Ding +10 more
doaj +2 more sources
Intermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions [PDF]
Frontiers in Molecular Biosciences, 2020 In bacterial cells we find a variety of interacting macromolecules, among them RNAs and proteins. Not only small regulatory RNAs (sRNAs), but also small proteins have been increasingly recognized as regulators of bacterial gene expression.
Inam Ul Haq +2 more
doaj +3 more sources
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 ...
Laura R. Newburn, K. Andrew White
doaj +2 more sources
Intragenomic Long-Distance RNA–RNA Interactions in Plus-Strand RNA Plant Viruses [PDF]
Frontiers in Microbiology, 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.
Tamari Chkuaseli, K. Andrew White
doaj +2 more sources
Protocol for profiling virus-to-host RNA-RNA interactions in infected cells by RIC-seq [PDF]
STAR ProtocolsSummary: 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.
Zhaokui Cai, Hailian Zhao, Yuanchao Xue
doaj +2 more sources
Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network [PDF]
Cell Reports, 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 ...
Valerie Le Sage +5 more
doaj +2 more sources