Zhang Jingchao, Donahue Greg, Gilbert Michael B, Lapidot Tomer, Nicetto Dario, Zaret Kenneth S
Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
Nat Cell Biol. 2024 Dec;26(12):2115-2128. doi: 10.1038/s41556-024-01547-z. Epub 2024 Oct 31.
H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A 'binary switch' governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.
由赖氨酸甲基转移酶（KMTs）建立并由异染色质蛋白1（HP1）亚型压缩的H3K9me3异染色质，可抑制替代谱系基因和DNA重复序列。我们目前对H3K9me3异染色质稳定性的理解仅限于单个结构域和DNA重复序列。在这里，我们构建了Suv39h2基因敲除的小鼠胚胎干细胞，使其在1小时内降解剩余的两种H3K9me3 KMTs，并发现被动稀释和主动去除都有助于在12至24小时内H3K9me3的衰减。我们在全基因组中发现了四种不同的H3K9me3衰减率，以及可预测稳定性类别的染色质特征和转录因子结合模式。一个“二元开关”控制着异染色质的压缩，在KMT耗竭时，HP1会迅速从异染色质上解离，并且特定阈值水平的HP1会限制先驱因子的结合、染色质开放以及在12小时内从多能性状态退出。出乎意料的是，逐渐减少的H3K9me3结构域会揭示富含异染色质诱导蛋白的残余HP1β峰。我们的研究结果揭示了不同的H3K9me3异染色质维持动态，这些动态控制着基因网络和重复序列，共同维护多能性。
