DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis PMID: 32103174

ADC Targets in Oncology

2026-04-10

DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis

Nature. 2020 Mar;579(7798):291-296. doi: 10.1038/s41586-020-2041-2.

Zhengping Shao ^# ¹ ² , Ryan A Flynn ^# ³ , Jennifer L Crowe ^# ¹ ⁴ , Yimeng Zhu ^# ¹ ² , Jialiang Liang ⁵ , Wenxia Jiang ¹ ² , Fardin Aryan ⁵ , Patrick Aoude ⁵ , Carolyn R Bertozzi ³ ⁶ , Verna M Estes ¹ ² , Brian J Lee ¹ ² , Govind Bhagat ² ⁷ ⁸ ⁹ , Shan Zha ¹⁰ ¹¹ ¹² ¹³ ¹⁴ , Eliezer Calo ¹⁵ ¹⁶

Affiliations

1. Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
2. Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
3. Department of Chemistry, Stanford University, Stanford, CA, USA.
4. Graduate Program of Pathobiology and Molecular Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
5. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
6. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
7. Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
8. Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
9. Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
10. Institute for Cancer Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. [email protected].
11. Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. [email protected].
12. Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. [email protected].
13. Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. [email protected].
14. Department of Immunology and Microbiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. [email protected].
15. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
16. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
# Contributed equally.

Abstract

The DNA-dependent protein kinase (DNA-PK), which comprises the KU heterodimer and a catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor¹. KU binds to DNA ends, initiates cNHEJ, and recruits and activates DNA-PKcs. KU also binds to RNA, but the relevance of this interaction in mammals is unclear. Here we use mouse models to show that DNA-PK has an unexpected role in the biogenesis of ribosomal RNA (rRNA) and in haematopoiesis. The expression of kinase-dead DNA-PKcs abrogates cNHEJ². However, most mice that both expressed kinase-dead DNA-PKcs and lacked the tumour suppressor TP53 developed myeloid disease, whereas all Other previously characterized mice deficient in both cNHEJ and TP53 expression succumbed to pro-B cell lymphoma³. DNA-PK autophosphorylates DNA-PKcs, which is its best characterized substrate. Blocking the phosphorylation of DNA-PKcs at the T2609 cluster, but not the S2056 cluster, led to KU-dependent defects in 18S rRNA processing, compromised global protein synthesis in haematopoietic cells and caused bone marrow failure in mice. KU drives the assembly of DNA-PKcs on a wide range of cellular RNAs, including the U3 small nucleolar RNA, which is essential for processing of 18S rRNA⁴. U3 activates purified DNA-PK and triggers phosphorylation of DNA-PKcs at T2609. DNA-PK, but not Other cNHEJ factors, resides in nucleoli in an rRNA-dependent manner and is co-purified with the small subunit processome. Together our data show that DNA-PK has RNA-dependent, cNHEJ-independent functions during ribosome biogenesis that require the kinase activity of DNA-PKcs and its phosphorylation at the T2609 cluster.