H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA-seq]

We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration. Specifically, we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq, we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte-specific expression of a mutant form of histone 3 that is unable to be tri-methylated on lysine 27 (H3.3K27M), we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window, we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes, we observed significant increases in cardiomyocyte nucleation, a phenotype indicative of cytokinesis failures. In addition, nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together, our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3-mediated sarcomeric and actomyosin cytoskeletal gene repression.本研究鉴定了斑马鱼心脏内稳态心肌细胞与增殖型心肌细胞之间的全局转录组变化，并揭示了组蛋白H3第27位赖氨酸三甲基化（H3K27me3）沉积在促进心肌成功再生中的必需作用。具体而言，我们发现心肌细胞增殖过程伴随肌节与细胞骨架组分的下调，以及多梳家族甲基转移酶Ezh2的上调。通过染色质免疫共沉淀测序（ChIP-seq），我们证实该转录抑制现象与启动子区域新增的H3K27me3修饰沉积相关。我们构建了新型转基因斑马鱼品系，可实现心肌细胞特异性、诱导型表达赖氨酸27位无法发生三甲基化的组蛋白H3突变体（H3.3K27M），借此发现H3K27me3标记的沉积对于体内心脏再生至关重要。在再生窗口期的早期阶段，我们观察到表达H3.3K27M的伤口边缘心肌细胞异常维持肌节与肌动球蛋白基因的稳态表达水平，并表现出肌节结构的显著保留。尽管这些H3.3K27M心肌细胞的DNA复制过程正常进行，但我们观察到心肌细胞多核化现象显著增多，该表型提示存在胞质分裂失败。此外，由于新生心肌细胞无法定植至损伤区域，伤口边缘的核密度亦出现升高。综上，本研究揭示了新生心肌细胞的产生及其向损伤区域的定植，依赖于H3K27me3介导的肌节与肌动球蛋白细胞骨架基因抑制。

搜集汇总

背景与挑战

背景概述

该数据集是一个RNA-seq研究，聚焦于斑马鱼心脏再生过程中H3K27me3修饰对心肌细胞增殖和再生的调控机制。研究通过比较稳态和再生心肌细胞的转录组变化，发现H3K27me3在肌节和细胞骨架基因启动子上的沉积对心肌细胞胞质分裂和损伤浸润至关重要。数据集包含6个样本，覆盖再生和未损伤心肌细胞，使用Illumina HiSeq 2000平台进行测序，旨在揭示表观遗传修饰在心脏再生中的关键作用。