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Incorporation of a histone mutant with H3K56 site substitution perturbs the replication machinery in mouse embryonic stem cells
Xuan Kang1,* , Xiaomei Yang1 , Xiaobo Guo1 , Yabin Li1 , Chenxin Yang1 , Huimin Wei1,2,* , jianfeng Chang1,*
1Research Center for Translational Medicine, East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
2Tsingdao Advanced Research Institute, Tongji University, Qingdao 266071, China
*Correspondence to:Xuan Kang ,; Huimin Wei ,; jianfeng Chang ,
J Mol Cell Biol, Volume 14, Issue 3, March 2022, mjac014,
Keyword: H3K56A/M mutants, replication promotion, replication stress, transcriptional adaptation, mouse embryonic stem cells

Sense mutations in several conserved modifiable sites of histone H3 have been found to be strongly correlated with multiple tissue-specific clinical cancers. These clinical site mutants acquire a distinctively new epigenetic role and mediate cancer evolution. In this study, we mimicked histone H3 at the 56th lysine (H3K56) mutant incorporation in mouse embryonic stem cells (mESCs) by lentivirus-mediated ectopic expression and analyzed the effects on replication and epigenetic regulation. The data show that two types of H3K56 mutants, namely H3 lysine 56-to-methionine (H3K56M) and H3 lysine 56-to-alanine (H3K56A), promote replication by recruiting more minichromosome maintenance complex component 3 and checkpoint kinase 1 onto chromatin compared with wild-type histone H3 and other site substitution mutants. Under this condition, the frequency of genomic copy number gain in H3K56M and H3K56A cells globally increases, especially in the Mycl1 region, a known molecular marker frequently occurring in multiple malignant cancers. Additionally, we found the disruption of H3K56 acetylation distribution in the copy-gain regions, which indicates a probable epigenetic mechanism of H3K56M and H3K56A. We then identified that H3K56M and H3K56A can trigger a potential adaptation to transcription; genes involved in the mitogen-activated protein kinase pathway are partially upregulated, whereas genes associated with intrinsic apoptotic function show obvious downregulation. The final outcome of ectopic H3K56M and H3K56A incorporation in mESCs is an enhanced ability to form carcinomas. This work indicates that H3K56 site conservation and proper modification play important roles in harmonizing the function of the replication machinery in mESCs.