Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release

Turan Tufan, Gamze Comertpay, Ambra Villani, Geoffrey M. Nelson, Marina Terekhova, Shannon Kelley, Pavel Zakharov, Rochelle M. Ellison, Oleg Shpynov, Michael Raymond, Jerry Sun, Yitan Chen, Enno Bockelmann, Marta Stremska, Lance W. Peterson, Laura Boeckaerts, Seth R. Goldman, J. Iker Etchegaray, Maxim N. Artyomov, Francesca Peri and Kodi S. Ravichandran ()
Additional contact information
Turan Tufan: Washington University School of Medicine
Gamze Comertpay: Washington University School of Medicine
Ambra Villani: University of Zurich
Geoffrey M. Nelson: Harvard Medical School
Marina Terekhova: Washington University School of Medicine
Shannon Kelley: Washington University School of Medicine
Pavel Zakharov: Washington University School of Medicine
Rochelle M. Ellison: Washington University School of Medicine
Oleg Shpynov: Washington University School of Medicine
Michael Raymond: University of Virginia
Jerry Sun: Washington University School of Medicine
Yitan Chen: Washington University School of Medicine
Enno Bockelmann: University of Zurich
Marta Stremska: Washington University School of Medicine
Lance W. Peterson: Washington University in St. Louis
Laura Boeckaerts: Ghent University
Seth R. Goldman: Harvard Medical School
J. Iker Etchegaray: Washington University School of Medicine
Maxim N. Artyomov: Washington University School of Medicine
Francesca Peri: University of Zurich
Kodi S. Ravichandran: Washington University School of Medicine

Nature, 2024, vol. 628, issue 8007, 408-415

Abstract: Abstract During development, inflammation or tissue injury, macrophages may successively engulf and process multiple apoptotic corpses via efferocytosis to achieve tissue homeostasis1. How macrophages may rapidly adapt their transcription to achieve continuous corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved mechanism, in which RNA polymerase (Pol) II initiates transcription for 20–60 nucleotides, is paused for minutes to hours and is then released to make full-length mRNA2. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release to unleash a rapid transcriptional response. For human and mouse macrophages, the Pol II pause/release was required for continuous efferocytosis in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede Fc receptor-mediated phagocytosis, yeast uptake or bacterial phagocytosis. Integration of data from three genomic approaches—precision nuclear run-on sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-seq)—on efferocytic macrophages at different time points revealed that Pol II pause/release controls expression of select transcription factors and downstream target genes. Mechanistic studies on transcription factor EGR3, prominently regulated by pause/release, uncovered EGR3-related reprogramming of other macrophage genes involved in cytoskeleton and corpse processing. Using lysosomal probes and a new genetic fluorescent reporter, we identify a role for pause/release in phagosome acidification during efferocytosis. Furthermore, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing phagosomes, supporting defective corpse processing. Collectively, these data indicate that macrophages use Pol II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpses and for successive efferocytosis.

Date: 2024
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DOI: 10.1038/s41586-024-07172-y

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