RBP-Maps enables robust generation of splicing regulatory maps

• DOI: 10.1261/rna.069237.118
• Publication Date: 2018-11-09T16:58:49Z
• Authors: Brian A. Yee; Gabriel A. Pratt; Brenton R. Graveley; Eric L. Van Nostrand; Gene W. Yeo
• Keywords: 0303 health sciences; Bioinformatics; Sequence Analysis, RNA; Computational Biology; RNA-Binding Proteins; Alternative Splicing; 03 medical and health sciences; Gene Expression Regulation; Humans; Protein Isoforms; RNA Splice Sites; RNA, Messenger; Software

Alternative splicing of pre-messenger RNA transcripts enables the generation multiple protein isoforms from same gene locus, providing a major source diversity in mammalian genomes. binding proteins (RBPs) bind to control splice site choice and define which exons are included resulting mature transcript. However, depending on where RBPs relative sites, they can activate or repress usage. To explore this position-specific regulation, vivo sites identified by methods such as cross-linking immunoprecipitation (CLIP) integrated with alternative events RNA-seq microarray. Merging these data sets “splicing map,” CLIP signal merged meta-exon provides simple summary effect regulation. Here, we provide RBP-Maps, software tool simplify maps enable researchers rapidly query regulatory patterns an RBP interest. Further, discuss various approaches generate maps, focusing how decisions construction (such use peak versus read density, whole-reads only single-nucleotide candidate crosslink positions) affect interpretation using example eCLIP 150 profiled ENCODE consortium.