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

ABSTRACT: The regulation of gene expression is governed at multiple levels of chromatin organization. However, how gene regulation is coordinated remains relatively unexplored. Here we develop Dam&ChIC, a method that enables retrospective and multifactorial chromatin profiling in single cells. Dam&ChIC employs in vivo chromatin labeling with m6A to acquire a past chromatin state, coupled with an antibody-mediated readout to capture the present chromatin state. Analyses of diverse chromatin combinations highlight its versatility and superior resolution. By tracking LAD inheritance over the cell cycle, we showcase that Dam&ChIC provides retrospective single-cell chromatin data. Importantly, by applying Dam&ChIC in random X chromosome inactivation, we disentangle the temporal order of chromatin remodeling events. Our data reveals that upon mitotic exit, the inactive X chromosome undergoes extensive genome-lamina detachment, preceding H3K27me3 spreading. We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of gene-regulatory events underlying cell-state changes during development.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE288852 | GEO | 2025/04/01

REPOSITORIES: GEO

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

Project description:The regulation of gene expression is governed at multiple levels of chromatin organization. How coordination between these levels is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that experimentally combines scDamID and sortChIC to enable time-resolved and single-cell chromatin profiling at high resolution. Analysis of genome lamina associated domains (LADs) in haploid cells, reveals highly dynamic spatial repositioning of small LADs during interphase and partial inheritance over mitosis. When applied to study random X-inactivation Dam&ChIC reveals that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with a remarkable detachment of the same domains from the nuclear lamina. We find that detachment precedes H3K27me3 accumulation on the Xi and occurs after the exit from mitosis. Domains that retain strong genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for LADs in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unravelling interconnectivity and the order of chromatin events that underlie cell-state changes in single cells.

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