title: Systematical identification of splicing regulatory cis-elements and cognate trans-factors.
abstract: The majority of human genes undergo alternative splicing to generate multiple isoforms with distinct functions. This process is generally controlled by cis-acting splicing regulatory elements (SREs) that recruit trans-acting factors to promote or inhibit the use of nearby splice sites. The growing interest in understanding the regulatory rules of splicing necessitates the systematic identification of these SREs and their cognate protein factors using experimental and computational approaches. Here we describe a strategy to identify and analyze both cis-acting SREs and trans-acting splicing factors. This strategy involves a cell-based screen to identify SREs from a random sequences library and a modified RNA affinity purification approach to unbiasedly identify the splicing factors. These methods can be adopted to identify splicing enhancers or silencers in both exons and introns, and can be extended to different cultured cells. The resulting SREs and splicing factors can be further analyzed with a series of computational and experimental approaches. This approach will help us to collect a molecular part-list for splicing regulation, providing a rich data source that enables a better understanding of the "splicing code".
authors: Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States. Electronic address: ywang@med.unc.edu.
authors: Yang
authors: Y
authors: Wang
authors: Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States. Electronic address: zefeng@med.unc.edu.
authors: Zefeng
authors: Z
authors: Wang
mesh_terms: D017398:Alternative Splicing; D002846:Chromatography, Affinity; D004742:Enhancer Elements, Genetic; D005091:Exons; D017930:Genes, Reporter; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D037941:Silencer Elements, Transcriptional
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: Exonic splicing silencers; Intronic splicing enhancers; Intronic splicing silencers; Splicing factors; Splicing regulatory elements
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