Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A–SF3b complex

• DOI: 10.1038/ncomms15522
• Publication Date: 2017-05-25T13:22:33Z
• Authors: Teng Teng; Jennifer HC Tsai; Xiaoling Puyang; Michael Seiler; Shouyong Peng; Sudeep Prajapati; Daniel Aird; Silvia Buonamici; Benjamin Caleb; Betty Chan; Laura Corson; Jacob Feala; Peter Fekkes; Baudouin Gerard; Craig Karr; Manav Korpal; Xiang Liu; Jason T. Lowe; Yoshiharu Mizui; James Palacino; Eunice Park; Peter G. Smith; Vanitha Subramanian; Zhenhua Jeremy Wu; Jian Zou; Lihua Yu; Agustin Chicas; Markus Warmuth; Nicholas Larsen; Ping Zhu
• Keywords: 0301 basic medicine; Adenosine; Cell Survival; Science; Crystallography, X-Ray; Article; Mass Spectrometry; 03 medical and health sciences; Humans; Cell Proliferation; Q; Cryoelectron Microscopy; Exons; HCT116 Cells; Phosphoproteins; Introns; Alternative Splicing; Mutation; Mutagenesis, Site-Directed; Epoxy Compounds; Myeloid Cell Leukemia Sequence 1 Protein; Macrolides; Fatty Alcohols; Carrier Proteins; Protein Binding

AbstractPladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates with the differential GC content between adjacent introns and exons. We determine the crystal structure of human PHF5A demonstrating that Y36 is located on a highly conserved surface. Analysis of the cryo-EM spliceosome Bact complex shows that the resistance mutations cluster in a pocket surrounding the branch point adenosine, suggesting a competitive mode of action. Collectively, we propose that PHF5A–SF3B1 forms a central node for binding to these splicing modulators.