Deubiquitinase USP47-stabilized splicing factor IK regulates the splicing of ATM pre-mRNA

Abstract

IK depletion leads to an aberrant mitotic entry because of chromosomal misalignment through the enhancement of Aurora B activity at the interphase. Here, we demonstrate that IK, a spliceosomal component, plays a crucial role in the proper splicing of the ATM pre-mRNA among other genes related with the DNA Damage Response (DDR). Intron 1 in the ATM pre-mRNA, having lengths <200 bp, was not spliced in the IK-depleted cells and led to a deficiency of the ATM protein. Subsequently, the IK depletion-induced ATM protein deficiency impaired the ability to repair the damaged DNA. Because the absence of SMU1 results in IK degradation, the mechanism underlying IK degradation was exploited. IK was ubiquitinated in the absence of SMU1 and then subjected to proteolysis through the 26S proteasome. To prevent the proteolytic degradation of IK, a deubiquitinating enzyme, USP47, directly interacted with IK and stabilized it through deubiquitination. Collectively, our results suggest that IK is required for proper splicing of the ATM pre-mRNA and USP47 contributes toward the stabilization of IK.

Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia

“…6a ). In agreement with previous studies that USP47 is involved in the DNA damage repair pathway 26 , 43 , USP47 knockdown significantly increases γH 2 AX and ATR phosphorylation (Ser428) in CML cells (Fig. 6b ).…”

“…Consistent with previous reports 26 , 43 , we found that USP47 is involved in the DNA damage repair in CML cells. We further demonstrated that YB-1, a novel substrate of USP47, contributes to USP47-mediated DNA damage repair.…”

Loss of splicing factor IK impairs normal skeletal muscle development

“…Recently, IK has been reported to alleviate structural constraints that prevent the activation of spliceosomes formed on introns with a short 5′SS–BS distance during spliceosome activation in HeLa cells [ 14 ]. Besides, IK participates in a variety of cellular processes, such as cell cycle progression [ 11 ] and genome stability [ 32 ], and regulates influenza virus gene expression by binding to the viral RNA polymerase [ 13 ]. Although the role of IK has been studied previously in vitro, little is known about how IK functions in vivo.…”

Role of deubiquitinating enzymes in DNA double-strand break repair

“…Here, we will discuss the role of DUBs in DNA DSBR. Ka et al, 2020Cai et al, 2018Wang et al, 2016Dong et al, 2003Sobhian et al, 2007;Wang and Elledge, 2007;Cooper et al, 2009;Shao et al, 2009;Feng et al, 2010;Hu X et al, 2011Juang et al, 2012Sato et al, 2012;Wiener et al, 2012Altun et al, 2015Wu ZQ et al, 2019Li et al, 2019Luo et al, 2016Butler et al, 2012Ismail et al, 2014 DUB: deubiquitinating enzyme; USP: ubiquitin-specific protease; BRCA: breast cancer susceptibility; BRCC36: BRCA1/2-containing complex 36; OTUB: otubain; OTUD: ovarian tumor domain-containing protein; UCHL3: ubiquitin C-terminal hydrolase L3; POH1: Pad1 homologue; BAP1: BRCA1-associated protein 1; CHK: checkpoint kinase; RNF: RING finger protein; MRN: meiotic recombination 11 (MRE11)/DNA repair protein RAD50 homolog (RAD50)/Nijmegen breakage syndrome 1 (NBS1); TIP60: Tat-interactive protein-60 kDa; MDC1: mediator of DNA damage checkpoint protein 1; PALB2: partner and localizer of BRCA 2; RAP80: receptor-associated protein 80; PIRH2: p53 induced RING-H2 protein; HDAC1: histone deacetylase 1; RPA: replication protein A; CtIP: CtBP-interacting protein; H2AK13,15ub: ubiquitylation on histone H2A at K13 and K15; E2s: E2 ubiquitin enzymes.…”

“…Depleting IK can induce ATM protein deficiency. USP47 is reported to interact directly with IK and stabilize it through deubiquitination (Ka et al, 2020). Moreover, a recent study revealed that ovarian tumor domaincontaining protein 4 (OTUD4) regulates DNA repair and radio-sensitivity in non-small cell lung cancer (NSCLC) cells via ATM/CHK2/p53 signaling (Wu ZQ et al, 2019).…”