Intestinal perfusion induces rapid activation of immediate-early genes in weaning rats

C- fos and c- jun are immediate-early genes (IEGs) that are rapidly expressed after a variety of stimuli. Products of these genes subsequently bind to DNA regulatory elements of target genes to modulate their transcription. In rat small intestine, IEG mRNA expression increases dramatically after refeeding following a 48-h fast. We used an in vivo intestinal perfusion model to test the hypothesis that metabolism of absorbed nutrients stimulates the expression of IEGs. Compared with those of unperfused intestines, IEG mRNA levels increased up to 11 times after intestinal perfusion for 0.3–4 h with Ringer solutions containing high (100 mM) fructose (HF), glucose (HG), or mannitol (HM). Abundance of mRNA returned to preperfusion levels after 8 h. Levels of c- fos and c- jun mRNA and proteins were modest and evenly distributed among enterocytes lining the villi of unperfused intestines. HF and HM perfusion markedly enhanced IEG mRNA expression along the entire villus axis. The perfusion-induced increase in IEG expression was inhibited by actinomycin-D. Luminal perfusion induces transient but dramatic increases in c- fos and c- jun expression in villus enterocytes. Induction does not require metabolizable or absorbable nutrients but may involve de novo gene transcription in cells along the villus.

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Induction of immediate early genes after traumatic focal brain injury in the rat: Effects of mannitol on c-fos mRNA expression

Clinical Neurology and Neurosurgery ◽

10.1016/s0303-8467(97)81785-4 ◽

1997 ◽

Vol 99 ◽

pp. S115

Author(s):

Yohtaro Sakakibara ◽

Tatsuo Hayashi ◽

Yoshio Taguchi ◽

Yoshitaro Yamaguchi ◽

Hiroaki Sekino

Keyword(s):

Brain Injury ◽

Mrna Expression ◽

Immediate Early Genes ◽

Immediate Early ◽

Early Genes ◽

Focal Brain Injury

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Engineering combinatorial and dynamic decoders using synthetic immediate-early genes

10.1101/2019.12.17.880179 ◽

2019 ◽

Author(s):

Pavithran T. Ravindran ◽

Maxwell Z. Wilson ◽

Siddhartha G. Jena ◽

Jared E. Toettcher

Keyword(s):

Growth Factor ◽

Signaling Pathways ◽

Intracellular Signaling ◽

Target Genes ◽

Immediate Early Genes ◽

Immediate Early Gene ◽

Early Gene ◽

Immediate Early ◽

Specific Target ◽

Early Genes

AbstractFor tissues to grow and function properly, cells must coordinate actions such as proliferation, differentiation and apoptosis. This coordination is achieved in part by the activation of intracellular signaling pathways that trigger the expression of context-specific target genes. While the function of these natural circuits has been actively studied, synthetic biology provides additional powerful tools for deconstructing, repurposing, and designing novel signal-decoding circuits. Here we report the construction of synthetic immediate-early genes (synIEGs), target genes of the Erk signaling pathway that implement complex, user-defined regulation and can be monitored through the use of live-cell biosensors to track transcription and translation. We demonstrate the power and flexibility of this approach by confirming Erk duration-sensing by the FOS immediate-early gene, elucidating how the BTG2 gene is regulated by transcriptional activation and translational repression after growth-factor stimulation, and by designing a synthetic immediate-early gene that responds with AND-gate logic to the combined presence of growth factor and DNA damage stimuli. Our work paves the way to defining the molecular circuits that link signaling pathways to specific target genes, highlighting an important role for post-transcriptional regulation in signal decoding that may be masked by analyses of RNA abundance alone.

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BRD4 mediates NF-κB-dependent epithelial-mesenchymal transition and pulmonary fibrosis via transcriptional elongation

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00224.2016 ◽

2016 ◽

Vol 311 (6) ◽

pp. L1183-L1201 ◽

Cited By ~ 35

Author(s):

Bing Tian ◽

Yingxin Zhao ◽

Hong Sun ◽

Yueqing Zhang ◽

Jun Yang ◽

...

Keyword(s):

Pulmonary Fibrosis ◽

Nuclear Translocation ◽

Epithelial Mesenchymal Transition ◽

Immediate Early Genes ◽

Immediate Early ◽

Transcriptional Elongation ◽

Mesenchymal Transition ◽

Early Genes ◽

Chronic Lung Diseases

Chronic epithelial injury triggers a TGF-β-mediated cellular transition from normal epithelium into a mesenchymal-like state that produces subepithelial fibrosis and airway remodeling. Here we examined how TGF-β induces the mesenchymal cell state and determined its mechanism. We observed that TGF-β stimulation activates an inflammatory gene program controlled by the NF-κB/RelA signaling pathway. In the mesenchymal state, NF-κB-dependent immediate-early genes accumulate euchromatin marks and processive RNA polymerase. This program of immediate-early genes is activated by enhanced expression, nuclear translocation, and activating phosphorylation of the NF-κB/RelA transcription factor on Ser276, mediated by a paracrine signal. Phospho-Ser276 RelA binds to the BRD4/CDK9 transcriptional elongation complex, activating the paused RNA Pol II by phosphorylation on Ser2 in its carboxy-terminal domain. RelA-initiated transcriptional elongation is required for expression of the core epithelial-mesenchymal transition transcriptional regulators SNAI1, TWIST1, and ZEB1 and mesenchymal genes. Finally, we observed that pharmacological inhibition of BRD4 can attenuate experimental lung fibrosis induced by repetitive TGF-β challenge in a mouse model. These data provide a detailed mechanism for how activated NF-κB and BRD4 control epithelial-mesenchymal transition initiation and transcriptional elongation in model airway epithelial cells in vitro and in a murine pulmonary fibrosis model in vivo. Our data validate BRD4 as an in vivo target for the treatment of pulmonary fibrosis associated with inflammation-coupled remodeling in chronic lung diseases.

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Global Ischemia Induces Immediate-Early Genes Encoding Zinc Finger Transcription Factors

Journal of Cerebral Blood Flow & Metabolism ◽

10.1097/00004647-199607000-00005 ◽

1996 ◽

Vol 16 (4) ◽

pp. 557-565 ◽

Cited By ~ 57

Author(s):

Jari Honkaniemi ◽

Frank R. Sharp

Keyword(s):

Transcription Factors ◽

Dentate Gyrus ◽

Neuronal Death ◽

Immediate Early Genes ◽

Global Ischemia ◽

Immediate Early ◽

Mrna Levels ◽

Brain Areas ◽

Ca1 Neurons ◽

Early Genes

Ischemia induces immediate-early genes (IEGs) in brain. Since prolonged expression of some IEGs may precede neuronal death, some researchers have suggested that these IEGs mediate neuronal death. We therefore examined the effect of 5 and 10 min of global ischemia on the expression of the IEGs NGFI-A, NGFI-B, NGFI-C, egr-2, egr-3, and Nurr1 in gerbil brain. All of the IEGs were induced after 30 min of reperfusion in the hippocampus. Most of them were induced in several other regions as well, including cortex, hypothalamus, thalamus, and amygdala. The acute IEG induction decreased in most brain areas by 2–6 h. However, at 24 h following 5 min of ischemia NGFI-A continued to be expressed in the CA1 region and dentate gyrus. In the dentate gyrus, NGFI-C continued to be expressed for 24 h and egr-3 for as long as 72 h. In other brain areas, all of the IEGs returned to control levels by 72 h except in CA1, where most messenger RNA (mRNA) levels were decreased; this decrease correlated with marked neuronal loss. The persistent expression of NGFI-A in CA1 neurons destined to die and the persistent expression of NGFI-A, NGFI-C, and egr-3 genes in dentate granule cell neurons that survive may indicate that some transcription factors modulate cell death whereas others support cell survival when expressed for prolonged periods. The protein products of several transcription factors, including c- fos, are known to downregulate their own expression. The persistent expression of NGFI-A in the CA1 neurons destined to die could therefore be due to ischemia-induced transcriptional activation caused by, e.g., increased intracellular calcium levels plus a lack of negative feedback caused by the blockade of the translation of NGFI-A mRNA into protein.

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Cholesterogenic Lanosterol 14α-Demethylase (CYP51) Is an Immediate Early Response Gene

Endocrinology ◽

10.1210/en.2005-0781 ◽

2005 ◽

Vol 146 (12) ◽

pp. 5321-5331 ◽

Cited By ~ 21

Author(s):

Martina Fink ◽

Jure Ačimovič ◽

Tadeja Režen ◽

Nataša Tanšek ◽

Damjana Rozman

Keyword(s):

De Novo ◽

Regulatory Element ◽

Feedback Regulation ◽

Early Response ◽

Regulatory Elements ◽

Immediate Early ◽

Proximal Promoter ◽

Inducible Camp Early Repressor ◽

Sterol Regulatory Element

Lanosterol 14α-demethylase (CYP51) responds to cholesterol feedback regulation through sterol regulatory element binding proteins (SREBPs). The proximal promoter of CYP51 contains a conserved region with clustered regulatory elements: GC box, cAMP-response elements (CRE-like), and sterol regulatory element (SRE). In lipid-rich (SREBP-poor) conditions, the CYP51 mRNA drops gradually, the promoter activity is diminished, and no DNA-protein complex is observed at the CYP51-SRE1 site. The majority of cAMP-dependent transactivation is mediated through a single CRE (CYP51-CRE2). Exposure of JEG-3 cells to forskolin, a mediator of the cAMP-dependent signaling pathway, provokes an immediate early response of CYP51, which has not been described before for any cholesterogenic gene. The CYP51 mRNA increases up to 4-fold in 2 h and drops to basal level after 4 h. The inducible cAMP early repressor (ICER) is involved in attenuation of transcription. Overexpressed CRE-binding protein (CREB)/CRE modulator (CREM) transactivates the mouse/human CYP51 promoters containing CYP51-CRE2 independently of SREBPs, and ICER decreases the CREB-induced transcription. Besides the increased CYP51 mRNA, forskolin affects the de novo sterol biosynthesis in JEG-3 cells. An increased consumption of lanosterol, a substrate of CYP51, is observed together with modulation of the postlanosterol cholesterogenesis, indicating that cAMP-dependent stimuli cross-talk with cholesterol feedback regulation. CRE-2 is essential for cAMP-dependent transactivation, whereas SRE seems to be less important. Interestingly, when CREB is not limiting, the increasing amounts of SREBP-1a fail to transactivate the CYP51 promoter above the CREB-only level, suggesting that hormones might have an important role in regulating cholesterogenesis in vivo.

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Engineering combinatorial and dynamic decoders using synthetic immediate-early genes

Communications Biology ◽

10.1038/s42003-020-01171-1 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Pavithran T. Ravindran ◽

Maxwell Z. Wilson ◽

Siddhartha G. Jena ◽

Jared E. Toettcher

Keyword(s):

Intracellular Signaling ◽

Target Genes ◽

Immediate Early Genes ◽

Tissue Level ◽

Early Gene ◽

Immediate Early ◽

Early Genes ◽

Natural Target ◽

Context Specific ◽

External Stimuli

AbstractMany cell- and tissue-level functions are coordinated by intracellular signaling pathways that trigger the expression of context-specific target genes. Yet the input–output relationships that link pathways to the genes they activate are incompletely understood. Mapping the pathway-decoding logic of natural target genes could also provide a basis for engineering novel signal-decoding circuits. Here we report the construction of synthetic immediate-early genes (SynIEGs), target genes of Erk signaling that implement complex, user-defined regulation and can be monitored by using live-cell biosensors to track their transcription and translation. We demonstrate the power of this approach by confirming Erk duration-sensing by FOS, elucidating how the BTG2 gene is differentially regulated by external stimuli, and designing a synthetic immediate-early gene that selectively responds to the combination of growth factor and DNA damage stimuli. SynIEGs pave the way toward engineering molecular circuits that decode signaling dynamics and combinations across a broad range of cellular contexts.

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Feedback regulation by Atf3 in the endothelin-1-responsive transcriptome of cardiomyocytes: Egr1 is a principal Atf3 target

Biochemical Journal ◽

10.1042/bj20120125 ◽

2012 ◽

Vol 444 (2) ◽

pp. 343-355 ◽

Cited By ~ 24

Author(s):

Alejandro Giraldo ◽

Oliver P. T. Barrett ◽

Marcus J. Tindall ◽

Stephen J. Fuller ◽

Emre Amirak ◽

...

Keyword(s):

Negative Feedback ◽

Growth Response ◽

Target Genes ◽

Feedback Regulation ◽

Immediate Early Genes ◽

Immediate Early ◽

Cardiomyocyte Hypertrophy ◽

Negative Feedback Regulation ◽

Endothelin 1 ◽

Early Genes

Endothelin-1 promotes cardiomyocyte hypertrophy by inducing changes in gene expression. Immediate early genes including Atf3 (activating transcription factor 3), Egr1 (early growth response 1) and Ptgs2 (prostaglandin-endoperoxide synthase 2) are rapi-dly and transiently up-regulated by endothelin-1 in cardiomyocytes. Atf3 regulates the expression of downstream genes and is implicated in negative feedback regulation of other immediate early genes. To identify Atf3-regulated genes, we knocked down Atf3 expression in cardiomyocytes exposed to endothelin-1 and used microarrays to interrogate the transcriptomic effects. The expression of 23 mRNAs (including Egr1 and Ptgs2) was enhanced and the expression of 25 mRNAs was inhibited by Atf3 knockdown. Using quantitative PCR, we determined that knockdown of Atf3 had little effect on up-regulation of Egr1 mRNA over 30 min, but abolished the subsequent decline, causing sustained Egr1 mRNA expression and enhanced protein expression. This resulted from direct binding of Atf3 to the Egr1 promoter. Mathematical modelling established that Atf3 can suffice to suppress Egr1 expression. Given the widespread co-regulation of Atf3 with Egr1, we suggest that the Atf3–Egr1 negative feedback loop is of general significance. Loss of Atf3 caused abnormal cardiomyocyte growth, presumably resulting from the dysregulation of target genes. The results of the present study therefore identify Atf3 as a nexus in cardiomyocyte hypertrophy required to facilitate the full and proper growth response.

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Differential Expression of the Immediate Early Genes c-Fos, c-Jun, JunB, and NGFI-B in the Rat Brain following Transient Forebrain Ischemia

Journal of Cerebral Blood Flow & Metabolism ◽

10.1038/jcbfm.1994.27 ◽

1994 ◽

Vol 14 (2) ◽

pp. 206-216 ◽

Cited By ~ 99

Author(s):

Tobias Neumann-Haefelin ◽

Christoph Wießner ◽

Peter Vogel ◽

Tobias Back ◽

Konstantin-Alexander Hossmann

Keyword(s):

Metabolic Response ◽

Late Onset ◽

Immediate Early Genes ◽

Selective Vulnerability ◽

Brain Regions ◽

Global Ischemia ◽

Immediate Early ◽

Mrna Levels ◽

Early Genes ◽

Ca1 Region

The temporospatial expression pattern of four immediate early genes (IEGs) (c- fos, c- jun, junB, NGFI-B) following 30 min of global ischemia was investigated in rat brains by in situ hybridization and immunohistochemistry (c- fos). All examined IEG mRNAs, as well as Fos-like immunoreactivity, increased transiently in vulnerable and resistant brain regions following ischemia, but the induction profiles were distinct. Ischemia caused a post-ischemic early-onset, transient c- fos induction in widespread regions, as well as a late-onset induction restricted to vulnerable regions. Late-onset c- fos induction was observed in the CA1 region and the ventral thalamus but not in the striatum or neocortex, where neurons degenerate at a quicker pace. After recirculation, c- jun mRNA appeared to be initially coinduced with c- fos mRNA, but c- jun mRNA levels remained elevated or increased in various regions, including all vulnerable regions, when c- fos mRNA had already declined to near basal levels. Compared to c- fos and c- jun, junB induction was less pronounced and confined largely to the dentate gyrus. NGFI-B mRNA increased moderately and only in brain regions exhibiting the most dramatic c- fos increases and with similar kinetics. The differential activation of the investigated IEGs suggests that rather complex long-term adaptive processes may be initiated at the genomic level after global ischemia. The present findings provide further evidence that the activation of IEGs forms part of the brain's metabolic response to ischemia, but no simple correlation appears to exist between the induction of the investigated IEGs and the phenomenon of selective vulnerability.

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