scholarly journals Post-Transcriptional Circadian Regulation in Macrophages Organizes Temporally Distinct Immunometabolic States

2020 ◽  
Author(s):  
Emily J Collins ◽  
Mariana P Cervantes-Silva ◽  
George A Timmons ◽  
James R O’Siorain ◽  
Annie M Curtis ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Metabolic Regulation ◽  
Time Course ◽  
Mitochondrial Morphology ◽  
Circadian Regulation ◽  
Atp Production ◽  
Post Transcriptional Regulation ◽  
The Impact

SUMMARYOur core timekeeping mechanism, the circadian clock, regulates an astonishing amount of cellular physiology and behavior, playing a vital role in organismal fitness. While the mechanics of circadian control over cellular regulation can in part be explained by the transcriptional activation stemming from the positive arm of the clock’s transcription-translation negative feedback loop, research has shown that extensive circadian regulation occurs beyond transcriptional activation in fungal species and data suggest that this post-transcriptional regulation may also be preserved in mammals. To determine the extent to which circadian output is regulated post-transcriptionally in mammalian cells, we comprehensively profiled the transcriptome and proteome of murine bone marrow-derived macrophages in a high resolution, sample rich time course. We found that only 15% of the circadian proteome had corresponding oscillating mRNA and this regulation was cell intrinsic. Ontological analysis of oscillating proteins revealed robust temporal enrichment for protein degradation and translation, providing potential insights into the source of this extensive post-transcriptional regulation. We noted post-transcriptional temporal-gating across a number of connected metabolic pathways. This temporal metabolic regulation further corresponded with rhythms we observed in ATP production, mitochondrial morphology, and phagocytosis. With the strong interconnection between cellular metabolic states and macrophage phenotypes/responses, our work demonstrates that post-transcriptional circadian regulation in macrophages is broadly utilized as a tool to confer time-dependent immune function and responses. As macrophages coordinate many immunological and inflammatory functions, an understanding of this regulation provides a framework to determine the impact of circadian regulation on a wide array of disease pathologies.

Rhythmic post-transcriptional regulation of the circadian clock protein mPER2 in mammalian cells: A real-time analysis

2006 ◽  
Vol 401 (1-2) ◽  
pp. 44-48 ◽  
Author(s):  
Keigo Nishii ◽  
Iori Yamanaka ◽  
Maya Yasuda ◽  
Yota B. Kiyohara ◽  
Yoko Kitayama ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Circadian Clock ◽  
Real Time ◽  
Mammalian Cells ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Post Transcriptional Regulation ◽  
Clock Protein

scholarly journals A role for keratins in supporting mitochondrial organization and function in skin keratinocytes

2019 ◽  
Author(s):  
Kaylee Steen ◽  
Desu Chen ◽  
Fengrong Wang ◽  
Song Chen ◽  
Surinder Kumar ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Metabolic Regulation ◽  
Mouse Skin ◽  
Mitochondrial Morphology ◽  
Null Mouse ◽  
Embryonic Mouse ◽  
Atp Production ◽  
Skin Keratinocytes ◽  
Dynamics And Function ◽  
And Function

AbstractMitochondria fulfill essential roles in ATP production, metabolic regulation, calcium signaling, generation of reactive oxygen species (ROS) and additional determinants of cellular health. Recent studies have highlighted a role for mitochondria during cell differentiation, including in skin epidermis. The observation of oxidative stress in keratinocytes from Krt16 null mouse skin, a model for pachyonychia congenita (PC)-associated palmoplantar keratoderma, prompted us to examine the role of Keratin (K) 16 protein and its partner K6 in regulating the structure and function of mitochondria. Electron microscopy revealed major anomalies in mitochondrial ultrastructure in late stage, E18.5, Krt6a/Krt6b null embryonic mouse skin. Follow-up studies utilizing biochemical, metabolic, and live imaging readouts showed that, relative to controls, skin keratinocytes null for Krt6a/Krt6b or Krt16 exhibit elevated ROS, reduced mitochondrial respiration, intracellular distribution differences and altered movement of mitochondria within the cell. These findings highlight a novel role for K6 and K16 in regulating mitochondrial morphology, dynamics and function and shed new light on the causes of oxidative stress observed in PC and related keratin-based skin disorders.

scholarly journals Transcriptional regulation of stilbene synthases in grapevine germplasm differentially susceptible to downy mildew

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Mario Ciaffi ◽  
Anna Rita Paolacci ◽  
Marco Paolocci ◽  
Enrica Alicandri ◽  
Valentina Bigini ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Downy Mildew ◽  
Transcriptional Activation ◽  
Constitutive Expression ◽  
Stilbene Synthase ◽  
Disease Symptoms ◽  
Adaptive Resistance ◽  
Genes Encoding ◽  
The Impact ◽  
Stilbene Biosynthesis

Abstract Background To limit the impact of the downy mildew disease of grapevine and reduce the need to recur to chemical treatments, an effective strategy might be recovering adaptive resistance traits in both cultivated and wild V. vinifera germplasm. Considering that stilbenes represent the most important class of phytoalexins in the Vitaceae, the constitutive expression and transcriptional activation of all the functional members of the stilbene synthase gene family were analysed in a group of nine grapevine genotypes following artificial infection with the oomycete Plasmopara viticola, the causal agent of the disease. In addition, in the same genotypes we analyzed the expression of genes encoding for two transcription factors involved in the transcriptional regulation of the stilbene synthase genes, namely VvMYB14 and VvMYB15, and of genes encoding for chalcone synthases. Results Downy mildew incidence and severity ranged from nihil to high in the grapevine genotypes considered, being low to moderate in a subgroup of V. vinifera genotypes. The constitutive expression of the stilbene synthase genes as well as the extent of their transcriptional activation following P. viticola inoculation appeared to be inversely related to the proneness to develop disease symptoms upon infection. In a specular manner, following P. viticola inoculation all the chalcone synthase genes were up-regulated in the susceptible grapevine genotypes and down-regulated in the resistant ones. The infection brought by P. viticola appeared to elicit a co-ordinated and sequential transcriptional activation of distinct stilbene synthase genes subsets, each of which may be regulated by a distinct and specific MYB transcription factor. Conclusions The present results suggest that the induction of stilbene biosynthesis may contribute to the basal immunity against the downy mildew of grapevine, thus representing an adaptive resistance trait to recover, in both cultivated and wild V. vinifera germplasm. During the early stages of P. viticola infection, an antagonistic interaction between flavonol and stilbene biosynthesis might occur, whose outcome might determine the subsequent extent of disease symptoms. Further studies are needed to decipher the possible regulatory mechanisms involved in the antagonistic crosstalk between these two metabolic pathways in resistant and susceptible genotypes in response to P. viticola.

scholarly journals Porphyromonas gingivalis infection promotes mitochondrial dysfunction through Drp1-dependent mitochondrial fission in endothelial cells

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Tong Xu ◽  
Qin Dong ◽  
Yuxiao Luo ◽  
Yanqing Liu ◽  
Liang Gao ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Mitochondrial Dysfunction ◽  
Porphyromonas Gingivalis ◽  
Vascular Endothelial Cells ◽  
Mitochondrial Fission ◽  
Mitochondrial Morphology ◽  
Mitochondrial Fragmentation ◽  
Atp Production ◽  
Luminescence Assay ◽  
The Impact

AbstractPorphyromonas gingivalis (P. gingivalis), a key pathogen in periodontitis, has been shown to accelerate the progression of atherosclerosis (AS). However, the definite mechanisms remain elusive. Emerging evidence supports an association between mitochondrial dysfunction and AS. In our study, the impact of P. gingivalis on mitochondrial dysfunction and the potential mechanism were investigated. The mitochondrial morphology of EA.hy926 cells infected with P. gingivalis was assessed by transmission electron microscopy, mitochondrial staining, and quantitative analysis of the mitochondrial network. Fluorescence staining and flow cytometry analysis were performed to determine mitochondrial reactive oxygen species (mtROS) and mitochondrial membrane potential (MMP) levels. Cellular ATP production was examined by a luminescence assay kit. The expression of key fusion and fission proteins was evaluated by western blot and immunofluorescence. Mdivi-1, a specific Drp1 inhibitor, was used to elucidate the role of Drp1 in mitochondrial dysfunction. Our findings showed that P. gingivalis infection induced mitochondrial fragmentation, increased the mtROS levels, and decreased the MMP and ATP concentration in vascular endothelial cells. We observed upregulation of Drp1 (Ser616) phosphorylation and translocation of Drp1 to mitochondria. Mdivi-1 blocked the mitochondrial fragmentation and dysfunction induced by P. gingivalis. Collectively, these results revealed that P. gingivalis infection promoted mitochondrial fragmentation and dysfunction, which was dependent on Drp1. Mitochondrial dysfunction may represent the mechanism by which P. gingivalis exacerbates atherosclerotic lesions.

The impact of epitranscriptomic marks on post-transcriptional regulation in plants

2020 ◽  
Author(s):  
Xiang Yu ◽  
Bishwas Sharma ◽  
Brian D Gregory
Keyword(s):  
Transcriptional Regulation ◽  
Plant Development ◽  
Messenger Rna ◽  
Rna Modifications ◽  
Abiotic And Biotic Stresses ◽  
Rna Molecules ◽  
Biotic Stresses ◽  
Specific Mrnas ◽  
Post Transcriptional Regulation ◽  
The Impact

Abstract Ribonucleotides within the various RNA molecules in eukaryotes are marked with more than 160 distinct covalent chemical modifications. These modifications include those that occur internally in messenger RNA (mRNA) molecules such as N6-methyladenosine (m6A) and 5-methylcytosine (m5C), as well as those that occur at the ends of the modified RNAs like the non-canonical 5′ end nicotinamide adenine dinucleotide (NAD+) cap modification of specific mRNAs. Recent findings have revealed that covalent RNA modifications can impact the secondary structure, translatability, functionality, stability and degradation of the RNA molecules in which they are included. Many of these covalent RNA additions have also been found to be dynamically added and removed through writer and eraser complexes, respectively, providing a new layer of epitranscriptome-mediated post-transcriptional regulation that regulates RNA quality and quantity in eukaryotic transcriptomes. Thus, it is not surprising that the regulation of RNA fate mediated by these epitranscriptomic marks has been demonstrated to have widespread effects on plant development and the responses of these organisms to abiotic and biotic stresses. In this review, we highlight recent progress focused on the study of the dynamic nature of these epitranscriptome marks and their roles in post-transcriptional regulation during plant development and response to environmental cues, with an emphasis on the mRNA modifications of non-canonical 5′ end NAD+ capping, m6A and several other internal RNA modifications.

scholarly journals Long-term HIF-1α transcriptional activation is essential for heat-acclimation-mediated cross tolerance: mitochondrial target genes

2017 ◽  
Vol 312 (5) ◽  
pp. R753-R762 ◽  
Author(s):  
Rivka Alexander-Shani ◽  
Ahmad Mreisat ◽  
Elia Smeir ◽  
Gary Gerstenblith ◽  
Michael D. Stern ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Ischemia Reperfusion ◽  
Mitochondrial Gene ◽  
Lactate Production ◽  
Heat Acclimation ◽  
Cross Tolerance ◽  
Metabolic Switch ◽  
Atp Production ◽  
The Impact

An important adaptive feature of heat acclimation (HA) is the induction of cross tolerance against novel stressors (HACT) Reprogramming of gene expression leading to enhanced innate cytoprotective features by attenuating damage and/or enhancing the response of “help” signals plays a pivotal role. Hypoxia-inducible factor-1α (HIF-1α), constitutively upregulated by HA (1 mo, 34°C), is a crucial transcription factor in this program, although its specific role is as yet unknown. By using a rat HA model, we studied the impact of disrupting HIF-1α transcriptional activation [HIF-1α:HIF-1β dimerization blockade by intraperitoneal acriflavine (4 mg/kg)] on its mitochondrial gene targets [phosphoinositide-dependent kinase-1 (PDK1), LON, and cyclooxygenase 4 (COX4) isoforms] in the HA rat heart. Physiological measures of cardiac HACT were infarct size after ischemia-reperfusion and time to rigor contracture during hypoxia in cardiomyocytes. We show that HACT requires transcriptional activation of HIF-1α throughout the course of HA and that this activation is accompanied by two metabolic switches: 1) profound upregulation of PDK1, which reduces pyruvate entry into the mitochondria, consequently increasing glycolytic lactate production; 2) remodeling of the COX4 isoform ratio, inducing hypoxic-tolerant COX4.2 dominance, and optimizing electron transfer and possibly ATP production during the ischemic and hypoxic insults. LON and COX4.2 transcript upregulation accompanied this shift. Loss of HACT despite elevated expression of the cytoprotective protein heat shock protein-72 concomitantly with disrupted HIF-1α dimerization suggests that HIF-1α is essential for HACT. The role of a PDK1 metabolic switch is well known in hypoxia acclimation but not in the HA model and its ischemic setting. Remodeling of COX4 isoforms by environmental acclimation is a novel finding.

scholarly journals The circadian dynamics of small nucleolar RNA in the mouse liver

2017 ◽  
Vol 14 (130) ◽  
pp. 20170034 ◽  
Author(s):  
Stuart Aitken ◽  
Colin A. Semple
Keyword(s):  
Transcriptional Activation ◽  
Ribosome Biogenesis ◽  
Time Course ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Computational Method ◽  
Circadian Regulation ◽  
Small Nucleolar Rna ◽  
Rrna Maturation ◽  
Nucleolar Rna

The circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification. More generally, we find the abundance of snoRNA known to modify 18S and 28S to be inversely correlated with the abundance of their target. Cyclic patterns in the expression of a number of snoRNA indicate a coordination with rRNA maturation, potentially through an upregulation in their biogenesis, or their release from mature rRNA at the end of the previous cycle of rRNA maturation, in antiphase with the diurnal peak in pre-rRNA. Few cyclic snoRNA have cyclic host genes, indicating the action of regulatory mechanisms in addition to transcriptional activation of the host gene. For highly expressed independently transcribed snoRNA, we find a characteristic RNA polymerase II and H3K4me3 signature that correlates with mean snoRNA expression over the day.

scholarly journals Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection

2021 ◽  
Vol 22 (7) ◽  
pp. 3392
Author(s):  
Marina R. Alexander ◽  
Aaron M. Brice ◽  
Petrus Jansen van Vuren ◽  
Christina L. Rootes ◽  
Leon Tribolet ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Host Response ◽  
High Viral Load ◽  
Ribosome Profiling ◽  
Epithelial Cell Line ◽  
Transcriptional Level ◽  
Human Lung Epithelial Cell ◽  
Post Transcriptional Regulation ◽  
The Impact

The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, allowing tight control over potent host responses by both the host and the invading virus. Here, we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors (JUN, ZBTB20, ATF3, HIVEP2 and EGR1) as well as select antiviral cytokine genes, namely IFNB1, IFNL1,2 and 3, IL-6 and CCL5, that are restricted at the post-transcriptional level by SARS-CoV-2 infection and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection.

scholarly journals Post-transcriptional regulation of the content of spermidine/spermine N1-acetyltransferase by N1N12-bis(ethyl)spermine

1995 ◽  
Vol 305 (2) ◽  
pp. 451-458 ◽  
Author(s):  
L Parry ◽  
R Balaña Fouce ◽  
A E Pegg
Keyword(s):  
Transcriptional Regulation ◽  
Half Life ◽  
Mammalian Cells ◽  
Significant Proportion ◽  
Untranslated Regions ◽  
Translation Regulation ◽  
Polyamine Analogues ◽  
Post Transcriptional Regulation ◽  
Rate Limiting ◽  
Ssat Activity

Spermidine/spermine N1-acetyltransferase (SSAT) is the rate-limiting enzyme for the degradation and excretion of polyamines in mammalian cells, and its activity is known to be increased enormously on exposure to polyamines and polyamine analogues. The mechanism by which such an analogue, BESM [N1N12-bis(ethyl)spermine], increases the content of SSAT was investigated by transfecting COS-7 cells with plasmids containing SSAT cDNA in the pEUK expression vector. Despite a large increase in mRNA production, there was only a very small increase in SSAT activity in the transfected cells. When BESM was added at 36 h after transfection, there was a large and very rapid increase in SSAT protein amounting to 380-fold in 12 h without any increase in the mRNA. SSAT protein turned over very rapidly, with a half-life of about 20 min. In the presence of BESM, this turnover was greatly reduced, and the half-life increased to more than 13 h. However, this increase was not sufficient to account for all of the increase in SSAT protein, suggesting that there is also regulation of the translation of the mRNA by BESM. Further evidence for such translation regulation was obtained by studying the polysomal distribution of the SSAT mRNA. In the absence of BESM, most of the mRNA was present in fractions which sedimented more slowly than the monoribosome peak. In BESM-treated cells, a significant proportion of the SSAT mRNA was moved into the small-polysome region of the gradient. The expression of SSAT and the effects of BESM on the polysomal distribution of SSAT mRNA were not affected by the 5′- or 3′-untranslated regions of the mRNA, since constructs which lacked all of these regions gave similar results to constructs containing the entire mRNA sequence. These results show that the increased transcription of the SSAT gene that occurs in the presence of polyamine analogues such as BESM is not sufficient for SSAT expression and that post-transcriptional regulation is critical for the control of SSAT content.

scholarly journals Genome-wide dynamics of RNA synthesis, processing and degradation without RNA metabolic labeling

2019 ◽  
Author(s):  
Mattia Furlan ◽  
Eugenia Galeota ◽  
Nunzio Del Gaudio ◽  
Erik Dassi ◽  
Michele Caselle ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Steady State ◽  
Time Course ◽  
Rna Synthesis ◽  
Computational Method ◽  
Metabolic Labeling ◽  
Experimental Conditions ◽  
Rna Dynamics ◽  
Kinetic Rates ◽  
Post Transcriptional Regulation

AbstractThe kinetic rates of RNA synthesis, processing and degradation determine the dynamics of transcriptional regulation by governing both the abundance and the responsiveness to modulations of premature and mature RNA species. The study of RNA dynamics is largely based on the integrative analysis of total and nascent transcription, with the latter being quantified through RNA metabolic labeling. We describe here INSPEcT-, a computational method based on mathematical modeling of intronic and exonic expression, able to derive the dynamics of transcription from steady state or time course profiling of just total RNA, without requiring any information on nascent transcripts. Our approach closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcripts half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions where nascent transcription cannot be readily profiled. Finally, we applied INSPEcT- to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady state or time course data, with or without the profiling of nascent RNA.

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