@article{Sutandy_Ebersberger_Huang-vitro_iCLIP_model-2018,
author = {Sutandy, F. X. Reymond and Ebersberger, Stefanie and Huang, 
          Lu and Busch, Anke and Bach, Maximilian and Kang, Hyun-Seo 
          and Fallmann, Jörg and Maticzka, Daniel and Backofen, Rolf 
          and Stadler, Peter F. and Zarnack, Kathi and Sattler, 
          Michael and Legewie, Stefan and Konig, Julian},
title = {In vitro {iCLIP}-based modeling uncovers how the splicing 
         factor {U2AF2} relies on regulation by cofactors},
journal = {Genome Res},
year = {2018},
doi = {10.1101/gr.229757.117},
volume = {},
user = {backofen},
pmid = {29643205},
pages = {},
number = {},
issn = {1088-9051},
abstract = {Alternative splicing generates distinct mRNA isoforms and 
            is crucial for proteome diversity in eukaryotes. The 
            RNA-binding protein (RBP) U2AF2 is central to splicing 
            decisions, as it recognizes 3' splice sites and recruits the 
            spliceosome. We establish "in vitro iCLIP" experiments, in 
            which recombinant RBPs are incubated with long transcripts, 
            to study how U2AF2 recognizes RNA sequences and how this is 
            modulated by trans-acting RBPs. We measure U2AF2 affinities 
            at hundreds of binding sites and compare in vitro and in 
            vivo binding landscapes by mathematical modeling. We find 
            that trans-acting RBPs extensively regulate U2AF2 binding in 
            vivo, including enhanced recruitment to 3' splice sites and 
            clearance of introns. Using machine learning, we identify 
            and experimentally validate novel trans-acting RBPs 
            (including FUBP1, CELF6, and PCBP1) that modulate U2AF2 
            binding and affect splicing outcomes. Our study offers a 
            blueprint for the high-throughput characterization of in 
            vitro mRNP assembly and in vivo splicing regulation.}
}