Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (ATAC-Seq)
Macrophages can adjust their phenotype and function in response to environmental cues, such as encountering apoptotic cells or pathogens. After tissue injury or inflammation, macrophages must successively engulf and process multiple apoptotic corpses (via efferocytosis) to achieve tissue homeostasis. How macrophages may rapidly adapt their transcription to achieve continued corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved process wherein RNA polymerase II (Pol II), after initiating transcription for 20-60 nucleotides, gets 'paused' for seconds to hours; paused Pol II then gets 'released' to complete transcription to make full-length mRNA. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release as a mechanism to unleash a rapid transcriptional response. For human and murine macrophages, the Pol II pause/release was crucial for continued efferocytosis of corpses in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede FcR-mediated phagocytosis, yeast uptake, or bacterial phagocytosis. Integrating data from three complementary genomic approaches of PRO-seq, RNA-seq, and ATAC-seq on efferocytic macrophages at different time points, we found that Pol II pause/release controls expression of select transcription factors and downstream target genes. Further mechanistic studies on transcription factor Egr3, one of the genes prominently affected by pause/release, uncovered Egr3-related reprogramming of macrophage genes involved in cytoskeleton and corpse processing. Via lysosomal probes and a newly designed genetic fluorescent reporter, we identify a key role for pause/release in phagosome acidification during efferocytosis. Further, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing endosomes, supporting a defect in corpse processing. Collectively, these data advance a novel concept that macrophages use Polymerase II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpse and for successive efferocytosis. Overall design: Hoxb8-derived macrophages were incubated with apoptotic cells for 15min, 30min, and 45min efferocytosis.