Similar Datasets
Project description: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.
2024-01-25 | GSE253577 | GEO
Project description: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.
2024-01-25 | GSE253576 | GEO
Project description: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.
2024-01-25 | GSE253574 | GEO
Project description:Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release
| PRJNA1066304 | ENA
Project description:Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (ATAC-Seq)
| PRJNA1066306 | ENA
Project description:Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (PRO-Seq)
| PRJNA1066308 | ENA
Project description:Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release (RNA-Seq)
| PRJNA1066307 | ENA
Project description:It is unclear how various factors functioning in the transcriptional elongation by RNA polymerase II (RNA Pol II) cooperatively regulate pause/release and productive elongation in living cells. Using an acute protein-depletion approach, we report that SPT6 depletion results in the release of paused RNA Pol II into gene bodies through an impaired recruitment of PAF1C. Short genes demonstrate a release with increased mature transcripts, whereas long genes are released but fail to yield mature transcripts, due to a reduced processivity resulting from both SPT6 and PAF1C loss. Unexpectedly, SPT6 depletion causes an association of NELF with the elongating RNA Pol II on gene bodies, without any observed functional significance on transcriptional elongation pattern, arguing against a role for NELF in keeping RNA Pol II in the paused state. Furthermore, SPT6 depletion impairs heat-shock-induced pausing, pointing to a role for SPT6 in regulating RNA Pol II pause/release through PAF1C recruitment.
| S-EPMC9714687 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-08-09 | GSE202190 | GEO
Project description:Recruitment of the RNA polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA-binding transcription factors is well recognized as a key regulatory step in gene expression. We report here that promoter-proximal pausing is a general feature of transcription by Pol II in mammalian cells and thus an additional step where regulation of gene expression occurs. This suggests that some transcription factors recruit the transcription apparatus to promoters, whereas others effect promoter-proximal pause release. Indeed, we find that the transcription factor c-Myc, a key regulator of cellular proliferation, plays a major role in Pol II pause release rather than Pol II recruitment at its target genes. We discuss the implications of these results for the role of c-Myc amplification in human cancer.
| S-EPMC2864022 | biostudies-literature