Abstract
Protein–RNA interactions are implicated in a number of physiological roles as well as diseases, with molecular mechanisms ranging from defects in RNA splicing, localization and translation to the formation of aggregates. Currently, ∼1400 human proteins have experimental evidence of RNA-binding activity. However, only ∼250 of these proteins currently have experimental data on their target RNAs from various sequencing-based methods such as eCLIP. To bridge this gap, we used an established, computationally expensive protein–RNA interaction prediction method, catRAPID, to populate a large database, RNAct. RNAct allows easy lookup of known and predicted interactions and enables global views of the human, mouse and yeast protein–RNA interactomes, expanding them in a genome-wide manner far beyond experimental data (http://rnact.crg.eu).
Highlights
RNA-binding proteins (RBPs) are key in RNA splicing, processing, export, localization and regulation of translation and are implicated in a number of pathologies in humans
Human proteins encoded by 1393 genes currently have experimental evidence of RNA-binding activity [4,5,6]
Normalizing the prediction score by sequence lengths, to a previous work [19], we found that the predictive performance decreases slightly
Summary
RNA-binding proteins (RBPs) are key in RNA splicing, processing, export, localization and regulation of translation and are implicated in a number of pathologies in humans. Human proteins encoded by 1393 genes currently have experimental evidence of RNA-binding activity [4,5,6]. These proteins contain one or more RNA-binding regions, either in the form of canonical globular domains or of more recently discovered, intrinsically disordered RNA interaction regions [7,8]. Our database covers the H. sapiens, M. musculus and S. cerevisiae genomes and contains a total of 5.87 billion pairwise interactions. RNAct makes available our genome-wide protein–RNA interaction predictions and combines them with powerful and intuitive search functionality, including pairwise search for sets of proteins and RNAs. The display is enriched with useful annotation, including transcript support level (TSL) and APPRIS classification for isoforms and RNA subcellular localization from the RNALocate database.
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