The local density of H3K9me3 dictates the stability of HP1α condensates-mediated genomic interactions

Ying Feng; Li Guo; Chen Yang; Hui Zheng; Xiao Xiao; Hanhui Ma

doi:10.1016/j.jgg.2023.04.006

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The local density of H3K9me3 dictates the stability of HP1α condensates-mediated genomic interactions

doi: 10.1016/j.jgg.2023.04.006

a
School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
b
Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
c
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China

Funds: This work was funded by the National Natural Science Foundation of China (No. 31970591 to H. Ma), the Shanghai Pujiang Program (19PJ1408000 to H. Ma) and the Shanghai Science and Technology Innovation Action Plan (21JC1404800 to H. Ma). We thank Luke Lavis (Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA) for the HaloTag JF-549. U2OS Genomic DNA was a gift from Xingxu Huang. We thank Pengwei Zhang and Shuangli Zhang for their help with cell sorting. DeltaVision Ultra microscopy was provided by the Shanghai Institute for Advanced Immunochemical Studied (SIAIS) at Shanghaitech University.

Received Date: 2023-01-01
Revised Date: 2023-04-10
Accepted Date: 2023-04-13

Available Online: 2023-04-26

Abstract

Abstract

The human genome can be demarcated into domains based on distinct epigenetic states. The trimethylation of histone H3 lysine 9 (H3K9me3) is essential for the formation of constitutive heterochromatin nanodomains. However, the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear. Here we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions. We select three loci (IDR3, TCF3, and PR1) with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous HP1α condensates. Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1α condensates. By dual-color labeling and long-term tracking of IDR3 and PR1 loci, we find a periodical association between the two ranging from one to three hours. Epigenetic perturbation-induced Genome organization (EpiGo)-KRAB introduces ∼20 kilobases of H3K9me3 at the TCF3 locus, which is sufficient to establish a stable association between TCF3 and HP1α condensates. In addition, EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3. Briefly, these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1α condensates.
- H3K9me3,
- HP1α,
- chromatin dynamics,
- genomic interaction,
- epigenetic perturbation

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References(28)

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