September 22, 2019  |  

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Authors: Funnell, Tyler and Tasaki, Shinya and Oloumi, Arusha and Araki, Shinsuke and Kong, Esther and Yap, Damian and Nakayama, Yusuke and Hughes, Christopher S and Cheng, S-W Grace and Tozaki, Hirokazu and Iwatani, Misa and Sasaki, Satoshi and Ohashi, Tomohiro and Miyazaki, Tohru and Morishita, Nao and Morishita, Daisuke and Ogasawara-Shimizu, Mari and Ohori, Momoko and Nakao, Shoichi and Karashima, Masatoshi and Sano, Masaya and Murai, Aiko and Nomura, Toshiyuki and Uchiyama, Noriko and Kawamoto, Tomohiro and Hara, Ryujiro and Nakanishi, Osamu and Shumansky, Karey and Rosner, Jamie and Wan, Adrian and McKinney, Steven and Morin, Gregg B and Nakanishi, Atsushi and Shah, Sohrab and Toyoshiba, Hiroyoshi and Aparicio, Samuel

CDC-like kinase phosphorylation of serine/arginine-rich proteins is central to RNA splicing reactions. Yet, the genomic network of CDC-like kinase-dependent RNA processing events remains poorly defined. Here, we explore the connectivity of genomic CDC-like kinase splicing functions by applying graduated, short-exposure, pharmacological CDC-like kinase inhibition using a novel small molecule (T3) with very high potency, selectivity, and cell-based stability. Using RNA-Seq, we define CDC-like kinase-responsive alternative splicing events, the large majority of which monotonically increase or decrease with increasing CDC-like kinase inhibition. We show that distinct RNA-binding motifs are associated with T3 response in skipped exons. Unexpectedly, we observe dose-dependent conjoined gene transcription, which is associated with motif enrichment in the last and second exons of upstream and downstream partners, respectively. siRNA knockdown of CLK2-associated genes significantly increases conjoined gene formation. Collectively, our results reveal an unexpected role for CDC-like kinase in conjoined gene formation, via regulation of 3'-end processing and associated splicing factors.The phosphorylation of serine/arginine-rich proteins by CDC-like kinase is a central regulatory mechanism for RNA splicing reactions. Here, the authors synthesize a novel small molecule CLK inhibitor and map CLK-responsive alternative splicing events and discover an effect on conjoined gene transcription.

Journal: Nature communications
DOI: 10.1038/s41467-016-0008-7
Year: 2017

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