Chromatin remodeling activity of EP400 safeguards chromosomal stability by preventing CENP-A mislocalization

  • Cell Rep. 2025 Oct 24;44(11):116423. doi: 10.1016/j.celrep.2025.116423.
Subhash Chandra Sethi  1 ,  Roshan L Shrestha  2 ,  Vinutha Balachandra  1 ,  Tetsuya Hori  3 ,  Luca Corda  4 ,  Shinjen Lin  5 ,  Laurent Ozbun  6 ,  Tatiana S Karpova  6 ,  Katherine McKinnon  7 ,  Raj Chari  8 ,  Gianluca Pegoraro  6 ,  Ken Chih-Chien Cheng  5 ,  Simona Giunta  4 ,  Natasha J Caplen  1 ,  Tatsuo Fukagawa  3 ,  Munira A Basrai  9
Affiliations
  • 1. Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD, USA.
  • 2. Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD, USA; Developmental Therapeutics Branch, NCI, NIH, Bethesda, MD, USA.
  • 3. Graduate School of Frontier Biosciences, The University of Osaka, Suita, Osaka, Japan.
  • 4. Laboratory of Genome Evolution, Sapienza University of Rome, Rome, Italy.
  • 5. Functional Genomics Laboratory, NCATS, NIH, Bethesda, MD, USA.
  • 6. Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, USA.
  • 7. CCR Vaccine Branch Flow Cytometry Core, NCI, NIH, Bethesda, MD, USA.
  • 8. Genome Modification Core (GMC), Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
  • 9. Genetics Branch, National Cancer Institute (NCI), NIH, Bethesda, MD, USA. Electronic address: [email protected].
PMID: 41138186 DOI: 10.1016/j.celrep.2025.116423
Abstract

The mislocalization of CENP-A to non-centromeric regions contributes to chromosomal instability (CIN). The NuA4 Histone Acetyltransferase complex members EP400 and KAT5 regulate histone H2A.Z-H2B exchange and acetylation of histones, respectively. Overexpression of CENP-A and mutations in NuA4 components are observed in cancers. Here, we define a role for the chromatin remodeling activity of EP400, a top hit in RNAi screens for increased nuclear levels of CENP-A, in preventing CENP-A mislocalization and CIN. Mechanistically, we demonstrate a defect in the extraction of CENP-A from chromatin in cells expressing the EP400K1085G mutant, which lacks ATPase activity for histone exchange. Consistent with these results, EP400K1085G cells show increased CENP-A enrichment in chromatin and mislocalization to non-centromeric regions. Importantly, EP400K1085G cells exhibit CIN phenotypes in stable, near-diploid RPE1 cells with wild-type p53. In summary, our findings expand the role of EP400 from nucleosome destabilization for histone exchange to preventing the stable association of CENP-A with non-centromeric regions and CIN.

Keywords
ATPase activity; CENP-A; CP: Molecular biology; EP400; KAT5; NuA4 HAT complex; centromere; chromatin remodeler; chromosomal instability; histone acetylation; kinetochore.
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