@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, Jorg 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},
  volume =	 {},
  number =	 {},
  pages =	 {},
  user =	 {backofen},
  pmid =	 {29643205},
  doi = 	 {10.1101/gr.229757.117},
  issn = 	 {1088-9051},
  issn = 	 {1549-5469},
  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.}
}