TY  - JOUR
A1  - Sutandy, F.X. Reymond
A1  - Ebersberger, Stefanie
A1  - Huang, Lu
A1  - Busch, Anke
A1  - Bach, Maximilian
A1  - Kang, Hyun-Seo
A1  - Fallmann, Jörg
A1  - Maticzka, Daniel
A1  - Backofen, Rolf
A1  - Stadler, Peter F.
A1  - Zarnack, Kathi
A1  - Sattler, Michael
A1  - Legewie, 
Stefan
A1  - König, Julian
T1  - In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
Y1  - 2018/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 699 
EP  - 713 
DO  - 10.1101/gr.229757.117 
VL  - 28 
IS  - 5 
UR  - http://genome.cshlp.org/content/28/5/699.abstract 
N2  - 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. 
ER  -