Stimulation-responsive enhancers regulate inflammatory gene activation through retention and modification of H2A.Z-variant accessible nucleosomes

Sporrij, A.; Prasad, M.; Muhire, B.; Fast, E. M.; Manning, M. E.; Choudhuri, A.; Weiss, J.; Koh, M.; Yang, S.; Kingston, R. E.; Tolstorukov, M.; Clevers, H.; Zon, L. I.

doi:10.1101/2022.09.12.507565

bioRxiv · 10.1101/2022.09.12.507565

Stimulation-responsive enhancers regulate inflammatory gene activation through retention and modification of H2A.Z-variant accessible nucleosomes

Sporrij, A.·Prasad, M.·Muhire, B.·Fast, E. M.·Manning, M. E.·Choudhuri, A.·Weiss, J.·Koh, M.·Yang, S.·Kingston, R. E.·Tolstorukov, M.·Clevers, H.·Zon, L. I.

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Abstract

Prostaglandin E2 (PGE2) and 16,16-dimethyl-PGE2 (dmPGE2) are important regulators of hematopoietic stem and progenitor cell (HSPC) fate and offer potential to enhance stem cell therapies1,2. The mechanism of gene regulation in response to dmPGE2 is poorly understood. Here, we show that dmPGE2 regulates inflammatory gene induction by modulating the chromatin architecture and activity of enhancer elements in human HSPCs. We identified the specific genomic reorganization at stimuli-responsive enhancers that permits rapid transcriptional activation. We found that dmPGE2-inducible enhancers retain MNase-accessible, H2A.Z-variant nucleosomes that are permissive to binding of the transcription factor CREB. CREB binding to enhancer nucleosomes is concomitant with deposition of the histone acetyltransferases p300 and Tip60 on chromatin. Subsequent H2A.Z acetylation improves chromatin accessibility at stimuli-responsive enhancers. Our findings support a model where histone variant nucleosomes retained within inducible enhancers facilitate transcription factor (TF) binding. Acetylation of histone variant nucleosomes by TF-associated nucleosome remodelers creates the accessible nucleosome landscape required for immediate enhancer activation and gene induction. Our work provides a mechanism by which inflammatory mediators such as dmPGE2 lead to acute transcriptional changes and alter HSPC behavior.

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Sporrij, A., Prasad, M., Muhire, B., Fast, E. M., Manning, M. E., Choudhuri, A., Weiss, J., Koh, M., Yang, S., Kingston, R. E., Tolstorukov, M., Clevers, H., Zon, L. I.. 2022-09-13. Stimulation-responsive enhancers regulate inflammatory gene activation through retention and modification of H2A.Z-variant accessible nucleosomes. https://doi.org/10.1101/2022.09.12.507565

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