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bioRxiv · 10.64898/2026.02.26.708215

FACT depletion results in a temporal cascade of chromatin disruption preceding transcriptional collapse in stem cells

Sankar, R.·Jackson, B. M.·Lardo, S. M.·Flury, V.·Groth, A.·Hainer, S. J.
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Abstract

The histone chaperone FACT is essential for chromatin organization and stem cell identity, yet the sequence of events through which FACT maintains chromatin integrity remains unclear. We generate a high-resolution temporal map of events leading to chromatin destabilization and cell identity loss in murine embryonic stem cells following dTAG-mediated depletion of FACT. Loss of FACT initiates a rapid cascade, with nucleosome phasing disruption and reduced H3K4me3 beginning within 10 minutes in a transcription-dependent manner. This architectural destabilization enables pluripotency transcription factors to ectopically occupy gene bodies. FACT loss results in RNA Polymerase II accumulation within 30 minutes and altered H3K36me3 deposition preceding a global transcriptional collapse at 2 hours of FACT depletion. FACT restoration fails to rescue these defects, demonstrating they are largely irreversible. Our findings define a temporal hierarchy in which FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse in stem cells.

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Sankar, R., Jackson, B. M., Lardo, S. M., Flury, V., Groth, A., Hainer, S. J.. 2026-02-27. FACT depletion results in a temporal cascade of chromatin disruption preceding transcriptional collapse in stem cells. https://doi.org/10.64898/2026.02.26.708215

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