SpliceAid-F: a database of human splicing factors and their RNA-binding sites

Abstract

A comprehensive knowledge of all the factors involved in splicing, both proteins and RNAs, and of their interaction network is crucial for reaching a better understanding of this process and its functions. A large part of relevant information is buried in the literature or collected in various different databases. By hand-curated screenings of literature and databases, we retrieved experimentally validated data on 71 human RNA-binding splicing regulatory proteins and organized them into a database called ‘SpliceAid-F’ (http://www.caspur.it/SpliceAidF/). For each splicing factor (SF), the database reports its functional domains, its protein and chemical interactors and its expression data. Furthermore, we collected experimentally validated RNA–SF interactions, including relevant information on the RNA-binding sites, such as the genes where these sites lie, their genomic coordinates, the splicing effects, the experimental procedures used, as well as the corresponding bibliographic references. We also collected information from experiments showing no RNA–SF binding, at least in the assayed conditions.In total, SpliceAid-F contains 4227 interactions, 2590 RNA-binding sites and 1141 ‘no-binding’ sites, including information on cellular contexts and conditions where binding was tested.The data collected in SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements.

Identifying Splicing Regulatory Elements with de Bruijn Graphs

“…We apply our model on a data set of all known human coding exons and their flanking intronic regions to find exonic enhancers and silencers. The discovered ESEs and ESSs overlap with many of the experimentally verified splicing elements in the SpliceAid-F database (Giulietti et al, 2013), as well as several computationally predicted data sets.…”

“…SpliceAid-F (Giulietti et al, 2013) is a recent comprehensive database that includes all the experimentally verified splicing factors and their binding sites. It contains 71 splicing factors and 655 binding sites for human.…”

“…To assess the significance of our predicted SREs and whether they are good candidates for ESEs or ESSs, we utilized the command-line version of Ontologizer (Bauer et al, 2008), with the goal of determining the enriched GO annotations for the experimentally verified SREs from SpliceAid-F (Giulietti et al, 2013) and checking whether our predicted SREs share the same enriched GO terms. This can be interpreted, as both sets of SREs affect the regulation of similar pathways.…”

“…CLIP has allowed the identification of the binding sites in vivo of several splicing factors, such as NOVA (Ule et al, 2003), SRSF1 (ASF/SF2) (Sanford et al, 2008), hnRNP A1 (Guil and Cáceres, 2007), and TDP-43 (Tollervey et al, 2011). There are at least 655 human splicing factor binding sites that are experimentally verified currently (Giulietti et al, 2013). The minigene-based technology utilizes the natural transcriptional and splicing machinery but concentrates only on a genomic segment of interest (Warner and Chamberlain, 2006).…”

“…As experimental evidence indicates, SREs should not be restricted to a fixed length. SpliceAid-F (Giulietti et al, 2013) is a recent comprehensive database that includes all known splicing factors and their experimentally determined binding sites, from which it is clear that the experimentally verified SREs vary in length. SpliceAid-F contains binding site sequences for different organisms.…”