Kefalopoulou Samy, Rullens Pim M J, de Luca Kim L, de Vries Sandra S, Korthout Tessy, van Oudenaarden Alexander, Zeller Peter, Kind Jop
Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands.
Oncode Institute, Utrecht, The Netherlands.
Nat Cell Biol. 2025 Jul 10. doi: 10.1038/s41556-025-01687-w.
The regulation of gene expression is governed at multiple levels of chromatin organization. However, how gene regulation is co-ordinated remains relatively unexplored. Here we develop Dam&ChIC, a method that enables retrospective and multifactorial chromatin profiling in single cells. Dam&ChIC employs chromatin labelling in living cells with A to acquire a past chromatin state, coupled with an antibody-mediated readout to capture the present chromatin state. Analyses of diverse factor combinations highlight its versatility and superior resolution. By tracking lamina-associated domain inheritance over the cell cycle, we showcase that Dam&ChIC provides retrospective single-cell chromatin data. When applied in random X chromosome inactivation, Dam&ChIC disentangles the temporal order of chromatin remodelling events. Upon mitotic exit and following Xist expression, the inactive X chromosome undergoes extensive genome-lamina detachment, preceding spreading of Polycomb. We anticipate that Dam&ChIC will be instrumental in unravelling the interconnectivity and order of gene-regulatory events underlying cell-state changes during development.
基因表达的调控在染色质组织的多个层面上受到控制。然而，基因调控是如何协调的仍相对未被探索。在这里，我们开发了Dam&ChIC，一种能够在单细胞中进行回顾性和多因素染色质分析的方法。Dam&ChIC利用活细胞中的染色质标记A来获取过去的染色质状态，并结合抗体介导的读数来捕获当前的染色质状态。对多种因子组合的分析突出了其多功能性和卓越的分辨率。通过跟踪细胞周期中与核纤层相关结构域的遗传，我们证明Dam&ChIC提供回顾性单细胞染色质数据。当应用于随机X染色体失活时，Dam&ChIC解开了染色质重塑事件的时间顺序。在有丝分裂退出后并在Xist表达之后，失活的X染色体经历广泛的基因组-核纤层分离，这发生在多梳蛋白扩散之前。我们预计Dam&ChIC将有助于揭示发育过程中细胞状态变化背后基因调控事件的相互联系和顺序。
