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

Subhash Chandra Sethi; Roshan L Shrestha; Vinutha Balachandra; Tetsuya Hori; Luca Corda; Shinjen Lin; Laurent Ozbun; Tatiana S Karpova; Katherine McKinnon; Raj Chari; Gianluca Pegoraro; Ken Chih-Chien Cheng; Simona Giunta; Natasha J Caplen; Tatsuo Fukagawa; Munira A Basrai

doi:10.1016/j.celrep.2025.116423

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

Cell Rep. 2025 Nov 25;44(11):116423. doi: 10.1016/j.celrep.2025.116423. Epub 2025 Oct 24.

Authors

Subhash Chandra Sethi¹, Roshan L Shrestha², Vinutha Balachandra¹, Tetsuya Hori³, Luca Corda⁴, Shinjen Lin⁵, Laurent Ozbun⁶, Tatiana S Karpova⁶, Katherine McKinnon⁷, Raj Chari⁸, Gianluca Pegoraro⁶, Ken Chih-Chien Cheng⁵, Simona Giunta⁴, Natasha J Caplen¹, Tatsuo Fukagawa³, Munira A Basrai⁹

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: basraim@nih.gov.

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 EP400^K1085G mutant, which lacks ATPase activity for histone exchange. Consistent with these results, EP400^K1085G cells show increased CENP-A enrichment in chromatin and mislocalization to non-centromeric regions. Importantly, EP400^K1085G 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.

Published by Elsevier Inc.

MeSH terms

Autoantigens* / metabolism
Cell Line
Centromere Protein A* / metabolism
Chromatin / metabolism
Chromatin Assembly and Disassembly*
Chromosomal Instability*
Chromosomal Proteins, Non-Histone* / metabolism
Histone Acetyltransferases* / genetics
Histone Acetyltransferases* / metabolism
Histones / metabolism
Humans
Tumor Suppressor Protein p53 / metabolism

Substances

Centromere Protein A
CENPA protein, human
Chromosomal Proteins, Non-Histone
Histones
Autoantigens
Histone Acetyltransferases
Chromatin
Tumor Suppressor Protein p53

Abstract

MeSH terms

Substances

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