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

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

Nature communications (2017-02-25)
Tyler Funnell, Shinya Tasaki, Arusha Oloumi, Shinsuke Araki, Esther Kong, Damian Yap, Yusuke Nakayama, Christopher S Hughes, S-W Grace Cheng, Hirokazu Tozaki, Misa Iwatani, Satoshi Sasaki, Tomohiro Ohashi, Tohru Miyazaki, Nao Morishita, Daisuke Morishita, Mari Ogasawara-Shimizu, Momoko Ohori, Shoichi Nakao, Masatoshi Karashima, Masaya Sano, Aiko Murai, Toshiyuki Nomura, Noriko Uchiyama, Tomohiro Kawamoto, Ryujiro Hara, Osamu Nakanishi, Karey Shumansky, Jamie Rosner, Adrian Wan, Steven McKinney, Gregg B Morin, Atsushi Nakanishi, Sohrab Shah, Hiroyoshi Toyoshiba, Samuel Aparicio
ABSTRACT

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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
T3-CLK, ≥98% (HPLC)
Sigma-Aldrich
T3-CLK-N, ≥98% (HPLC)
Sigma-Aldrich
Anti-SR protein family Antibody, clone 16H3, clone 16H3, from mouse