Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA498123 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8100060.fastq.gz | Fastqsanger.gz | |||
| SRR8100061.fastq.gz | Fastqsanger.gz | |||
| SRR8100052.fastq.gz | Fastqsanger.gz | |||
| SRR8100062.fastq.gz | Fastqsanger.gz | |||
| SRR8100053.fastq.gz | Fastqsanger.gz |
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Project description:Distal enhancers characterized by H3K4me1 mark play critical roles in developmental and transcriptional programs. However, potential roles of specific distal regulatory elements in regulating RNA Polymerase II (Pol II) promoter-proximal pause release remain poorly investigated. Here we report that a unique cohort of jumonji C domain-containing protein 6 (JMJD6) and bromodomain-containing protein 4 (Brd4) co-bound distal enhancers, termed anti-pause enhancers (A-PEs), regulate promoter-proximal pause release of a large subset of transcription units via long-range interactions. Brd4-dependent JMJD6 recruitment on A-PEs mediates erasure of H4R3me2(s), which is directly read by 7SK snRNA, and decapping/demethylation of 7SK snRNA, ensuring the dismissal of the 7SKsnRNA/HEXIM inhibitory complex. The interactions of both JMJD6 and Brd4 with the P-TEFb complex permit its activation and pause release of regulated coding genes. The functions of JMJD6/ Brd4-associated dual histone and RNA demethylase activity on anti-pause enhancers have intriguing implications for these proteins in development, homeostasis and disease. All Gro-seq(s) were designed to reveal the transcriptional targets of JMJD6 and Brd4, and assess the role of JMJD6 and Brd4 in Pol II promoter-proximal pause release. All ChIP-seq(s) were designed to understand the unique features, associated molecular mechanisms and functions of the anti-pause enhancers (A-PEs) discovered in the current study.
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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.
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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.
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Project description:Transcriptional regulation occurs via changes to rates of different biochemical steps of transcription, but it remains unclear which rates are subject to change upon biological perturbation. Biochemical studies have suggested that stimuli predominantly affect the rates of RNA polymerase II (Pol II) recruitment and polymerase release from promoter-proximal pausing. Single-cell studies revealed that transcription occurs in discontinuous bursts, suggesting that features of such bursts like frequency and intensity could also be regulated. We combined Pol II chromatin immunoprecipitation sequencing (ChIP-seq) and single-cell transcriptional measurements to show that an independently regulated burst initiation step is required before polymerase recruitment can occur. Using a number of global and targeted transcriptional regulatory perturbations, we showed that biological perturbations regulated both burst initiation and polymerase pause release rates but seemed not to regulate polymerase recruitment rate. Our results suggest that transcriptional regulation primarily acts by changing the rates of burst initiation and polymerase pause release.
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