2. Academic Validation
  3. 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

  • Nat Commun. 2017 Feb 23;8(1):7. doi: 10.1038/s41467-016-0008-7.
Tyler Funnell 1 2,  Shinya Tasaki 3,  Arusha Oloumi 1 2 4,  Shinsuke Araki 3,  Esther Kong 1 2,  Damian Yap 1 2,  Yusuke Nakayama 3,  Christopher S Hughes 5,  S-W Grace Cheng 5,  Hirokazu Tozaki 3,  Misa Iwatani 3,  Satoshi Sasaki 3,  Tomohiro Ohashi 3,  Tohru Miyazaki 3,  Nao Morishita 3,  Daisuke Morishita 3,  Mari Ogasawara-Shimizu 3,  Momoko Ohori 3,  Shoichi Nakao 3,  Masatoshi Karashima 3,  Masaya Sano 3,  Aiko Murai 3,  Toshiyuki Nomura 3,  Noriko Uchiyama 3,  Tomohiro Kawamoto 3,  Ryujiro Hara 3 6,  Osamu Nakanishi 3 7,  Karey Shumansky 1 2,  Jamie Rosner 1 2 8,  Adrian Wan 1 2,  Steven McKinney 1 2,  Gregg B Morin 5 9,  Atsushi Nakanishi 3,  Sohrab Shah 1 2,  Hiroyoshi Toyoshiba 10,  Samuel Aparicio 11 12
Affiliations

Affiliations

  • 1 Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada, V5Z 1L3.
  • 2 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada, V6T 2B5.
  • 3 Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
  • 4 Janssen Pharmaceuticals, Toronto, Ontario, Canada.
  • 5 Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada, V5Z 1L3.
  • 6 Fujirebio Inc., Tokyo, Japan.
  • 7 Department of Innovative Drug Discovery and Development, Japan Agency for Medical Research and Development, Osaka, Japan.
  • 8 Advanced Research Computing, University of British Columbia, Vancouver, British Columbia, Canada.
  • 9 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada, V6H 3N1.
  • 10 Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan. [email protected].
  • 11 Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada, V5Z 1L3. [email protected].
  • 12 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada, V6T 2B5. [email protected].
PMID: 28232751 DOI: 10.1038/s41467-016-0008-7
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.

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