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ePRINT: exonuclease assisted mapping of protein-RNA interactions [PDF]
Genome BiologyRNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules.
Sophie Hawkins +6 more
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Protein-RNA interactions important for Plasmodium transmission. [PDF]
PLoS Pathogens, 2019 Kelly T Rios, Scott E Lindner
doaj +5 more sources
RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions. [PDF]
J Mol BiolWe present RNAproDB (https://rnaprodb.usc.edu/), a new webserver, analysis pipeline, database, and highly interactive visualization tool, designed for protein-RNA complexes, and applicable to all forms of nucleic acid containing structures. RNAproDB computes several mapping schemes to place nucleic acid components and present protein-RNA interactions ...
Mitra R +6 more
europepmc +4 more sources
Template-Based Modeling of Protein-RNA Interactions. [PDF]
PLoS Computational Biology, 2016 Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered.
Jinfang Zheng +3 more
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Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners. [PDF]
Biochem Soc Trans, 2020 Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins (RBPs). However, defining the RNA sequences and structures that are selectively recognised by an RBP remains
Colantoni A +4 more
europepmc +4 more sources
Protein-RNA interactions: structural characteristics and hotspot amino acids. [PDF]
RNA, 2018 Structural information about protein–RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important.
Krüger DM, Neubacher S, Grossmann TN.
europepmc +7 more sources
Compendium of Methods to Uncover RNA-Protein Interactions In Vivo
Methods and Protocols, 2021 Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the ...
Mrinmoyee Majumder +1 more
doaj +3 more sources
Protein–RNA interactions: new genomic technologies and perspectives [PDF]
Nature Reviews Genetics, 2012 RNA-binding proteins are key players in the regulation of gene expression. In this Progress article, we discuss state-of-the-art technologies that can be used to study individual RNA-binding proteins or large complexes such as the ribosome. We also describe how these approaches can be used to study interactions with different types of RNAs, including ...
Nicholas Luscombe +2 more
exaly +3 more sources
irCLIP platform for efficient characterization of protein–RNA interactions [PDF]
Nature Methods, 2016 The complexity of transcriptome-wide protein-RNA interaction networks is incompletely understood. While emerging studies are greatly expanding the known universe of RNA-binding proteins, methods for the discovery and characterization of protein-RNA interactions remain resource intensive and technically challenging. Here we introduce a UV-C crosslinking
Ryan Flynn +2 more
exaly +3 more sources
Dynamic protein-RNA interactions in mediating splicing catalysis. [PDF]
Nucleic Acids Res, 2019 The spliceosome is assembled via sequential interactions of pre-mRNA with five small nuclear RNAs and many proteins. Recent determination of cryo-EM structures for several spliceosomal complexes has provided deep insights into interactions between spliceosomal components and structural changes of the spliceosome between steps, but information on how ...
Chung CS +5 more
europepmc +3 more sources