Hematopoietic Progenitor Cell Genome Sensing of Inflammation [CUT&Tag]

Genomes must adapt dynamically to alterations in the signaling milieu, including acute and chronic inflammation that transiently or permanently disrupt genome function. We investigated this problem with a human disorder caused by heterozygous mutations in GATA2, encoding a hematopoietic stem/progenitor cell regulator. GATA2 deficiency causes bone marrow failure in humans and mice and predisposes to leukemia in humans. GATA2-deficient murine progenitors are hypersensitive to Toll-Like Receptor (TLR)- and interferon-g-mediated inflammatory signaling, and downregulating the cell type-specific transcription factor PU.1 reduced TLR1/2- and IFNg-induced transcriptional responses. Genome sensing of inflammation involved inflammation-dependent recruitment of PU.1 to chromatin and PU.1 pre-occupying specific loci. Motifs for RUNX developmental regulators were enriched at TLR1/2-IFNg-activated genes in GATA2-deficient progenitors. Contrasting with the paradigm in which GATA2 and RUNX1 function cooperatively, their opposing activities were vital for integrating signaling and transcriptional mechanisms to endow a progenitor genome with the capacity to sense the inflammatory environment. For RNA-seq experiment: ER-HOXB8-immortalized hi-77-/- and hi-77-/-;Spi1URE-/- cells were treated with vehicle (0.1%BSA in PBS), IFNg, Pam3CSK4, or both agonists for 4 h. hi-77+/+ cells were treated with vehicle or combination of IFNg and Pam3CSK4 as controls. For CUT&Tag experiment: hi-77+/+, hi-77-/-, and hi-77-/-;Spi1URE-/- cells were treated with vehicle or combination of IFNg and Pam3CSK4 for 4 h.