LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

• Ninomiya, Kensuke

• Adachi, Shungo

• Natsume, Tohru

• Iwakiri, Junichi

• Terai, Goro

• Asai, Kiyoshi

• Hirose, Tetsuro

Abstract

A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de-phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.

Journal

• EMBO Journal

  EMBO Journal 39 (23), e102729-, 2020-02-03

  John Wiley & Sons

Keywords

• intron retention
• noncoding RNA
• nuclear stress bodies
• phosphorylation
• splicing factors

Details

• CRID: 1050285299903635712
• NII Article ID: 120006876293
• HANDLE: 2115/79022
• ISSN: 02614189
• Text Lang: en
• Article Type: journal article
• Data Source:
  • IRDB
  • CiNii Articles