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<p>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&amp;ChIC, a method that enables retrospective and multifactorial chromatin profiling in single cells. Dam&amp;ChIC employs chromatin labelling in living cells with <sup>m6</sup>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&amp;ChIC provides retrospective single-cell chromatin data. When applied in random X chromosome inactivation, Dam&amp;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&amp;ChIC will be instrumental in unravelling the interconnectivity and order of gene-regulatory events underlying cell-state changes during development.</p>

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Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月10日

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  • Samy Kefalopoulou,
  • Pim M. J. Rullens,
  • Kim L. de Luca,
  • Sandra S. de Vries,
  • Tessy Korthout,
  • Alexander van Oudenaarden,
  • Peter Zeller,
  • Jop Kind

摘要

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 m6A 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.