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bioRxiv · 10.1101/2023.12.15.571749

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

Kefalopoulou, S.·Rullens, P. M. J.·de Luca, K. L.·de Vries, S. S.·Korthout, T.·van Oudenaarden, A.·Zeller, P.·Kind, J.
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Abstract

The regulation of gene expression is governed at multiple levels of chromatin organization. However, how coordination is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that enables time-resolved and multifactorial chromatin profiling at high resolution in single cells. Analysis of genome-lamina interactions in haploid cells reveals highly dynamic spatial repositioning of small domains during interphase and partial inheritance over mitosis. Dam&ChIC applied to study random X-inactivation uncovers that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with remarkable genome-lamina detachment. We find that genome-lamina detachment precedes H3K27me3 accumulation on the Xi and occurs upon mitotic exit. Domains that retain genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for genome-lamina interactions in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of chromatin events underlying cell-state changes in single cells.

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Kefalopoulou, S., Rullens, P. M. J., de Luca, K. L., de Vries, S. S., Korthout, T., van Oudenaarden, A., Zeller, P., Kind, J.. 2023-12-15. Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation. https://doi.org/10.1101/2023.12.15.571749

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