School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
J Genet Genomics. 2023 Oct;50(10):776-785. doi: 10.1016/j.jgg.2023.04.006. Epub 2023 Apr 26.
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 Heterochromatin Protein 1 (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.
人类基因组可以根据不同的表观遗传状态划分为不同的结构域。组蛋白 H3 赖氨酸 9（H3K9me3）的三甲基化对于形成组成型异染色质纳米结构域至关重要。然而，基因组区域需要特定的 H3K9me3 密度或程度才能实现稳定相互作用的程度尚不清楚。在这里，我们利用基于 CRISPR 的 DNA 成像技术来研究内源性或外源性 H3K9me3 在染色质动力学和基因组相互作用中的作用。我们选择三个具有不同 H3K9me3 水平的基因座（IDR3、TCF3 和 PR1）来检查基因组相互作用及其与内源性异染色质蛋白 1（HP1α）浓缩物的关联。我们的结果表明，基因座处 H3K9me3 的水平与其与 HP1α 浓缩物的关联呈正相关。通过对 IDR3 和 PR1 基因座进行双色标记和长期跟踪，我们发现两者之间存在一个从一个到三个小时不等的周期性关联。表观遗传扰动诱导的基因组组织（EpiGo）-KRAB 在 TCF3 基因座上引入了约 20 千碱基的 H3K9me3，这足以在 TCF3 和 HP1α 浓缩物之间建立稳定的关联。此外，EpiGo 介导的 H3K9me3 也导致 IDR3 和 TCF3 之间的稳定基因组相互作用。简而言之，这些数据表明 H3K9me3 的密度可以决定基因组区域和 HP1α 浓缩物之间相互作用的稳定性。
