Abstract
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones for 173 human AS events. Every entry includes the interaction partners, interaction type, experimental methods, AS type, tissue specificity or disease-relevant information, a simple description of the functionally tested interaction in the AS event and references. The database can be queried easily using a web server (http://47.88.84.236/Miasdb). We display some interaction figures for several genes. With this database, users can view the regulation network describing AS events for 12 given genes.
Highlights
Since the discovery that the number of genes in a genome is not linearly correlated with the complexity and functional diversity of an organism, alternative splicing (AS) has increasingly attracted the interest of researchers
AS of pre-mRNAs is essential for regulating gene expression, as it alters the function of a gene in different tissues and developmental stages by generating various mRNA isoforms composed of different combinations of exons
By manually screening the literature, we retrieved experimentally validated interactions that regulate human AS events and assembled them into an online database called the database of molecular interactions associated with alternative splicing (MiasDB)
Summary
Since the discovery that the number of genes in a genome is not linearly correlated with the complexity and functional diversity of an organism, alternative splicing (AS) has increasingly attracted the interest of researchers. SpliceAid-F was established by screening the literature; it is currently the only database describing interactions between SFs and their RNA-binding sites [33]. This database includes many artificially mutated RNA elements and does not include any records related to proteins. By manually screening the literature, we retrieved experimentally validated interactions that regulate human AS events and assembled them into an online database called the database of molecular interactions associated with alternative splicing (MiasDB) (http://47.88.84.236/ Miasdb). Our database collected 938 human interactions between RNA elements, SFs, TFs, splicing-associated kinases and modified histones for 173 human AS events. MiasDB provides a comprehensive resource of AS interactions in humans, and this database will aid in uncovering the regulatory principles of splicing processes
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