scholarly journals P0515BRD4 PROTEIN REGULATES THE RESPONSES TO HYPOXIA TRIGGERED IN THE EXPERIMENAL RENAL DAMAGE

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Paula Diaz-Bulnes ◽  
Ramon M Rodriguez ◽  
Viviana Corte ◽  
Elisenda Banon ◽  
Marta Lazo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Renal Damage ◽  
Target Genes ◽  
Inflammatory Cell ◽  
Inflammatory Cell Infiltration ◽  
Cell Infiltration ◽  
Iri Model ◽  
Upr Pathway

Abstract Background and Aims Renal hypoxia is not only one of the most common causes of acute kidney injury, but also a critical mediator in the transition to chronic kidney disease. When the kidney is exposed to an insufficient supply of oxygen to meet demand, some adaptive mechanisms are triggered by the cells to maintain homeostasis. Induction of HIF-1α transcription factor and activation of unfolded protein response (UPR) pathway, as consequence of ER dysfunction, are both essential to mediate the cell survival. The UPR pathway is regulated by three major protein sensors (IRE1α, PERK and ATF6) which under ER stress initiate the activation of the XBP1, ATF4 and ATF6 transcription factors, respectively. However, inappropriate activation of these mechanisms could lead to the enhanced transcription of genes involved in key processes in renal damage (inflammation, cell death or autophagy). On the other hand, BRD4 is an epigenetic reader that recognizes acetylated lysine residues on histone and other proteins, and mediates the binding of transcription factors to the transcriptional machinery. Our aim was to investigate whether BRD4-mediated epigenetic mechanisms could modulate the response to hypoxia triggered in acute renal damage. Method Tubular epithelial cell line, HK2, was cultured with thapsigargin (Tg) or in hypoxia chamber (1% O2, 5% CO2). In addition, these cells were treated with specific BET proteins inhibitors (JQ1, I-BET762) and with small interfering RNAs (siRNA BRD4, p300), or were subjected to knockdown of ATF4 and XBP1 by CRISPR/cas9 technology. Transcriptional changes were analyzed in each condition by RNA-sequencing. The binding of BRD4 to target genes and recruitment of the transcriptional machinery was analyzed by chromatin immunoprecipitation (ChIP) with specific antibodies against BRD4, RNA PolII, AcH3 and AcH4. Effect of JQ1 inhibitor was assayed in an ischemia/reperfusion injury (IRI) model, and analysis of gene expression, inflammatory cell infiltration, and epigenetic remodeling was carried out by quantitative PCR, IHQ and ChIP assay, respectively. Results Treatment of HK2 cells with BETs inhibitors, previously cultured with Tg or under hypoxia conditions, inhibits the gene expression of the GPR78 ER chaperon, and the XBP1 and ATF4 transcription factors modulating the downstream signaling pathways. Meanwhile, ATF6 expression remains unchanged. Gene silencing with siRNA and ChIP assays reveal that under activation of the UPR pathway or hypoxia, BRD4 recognizes acetylated histones in the GPR78, ATF4 and XBP1 promoters, recruits the pTEF-b complex and activates RNA-pol II allowing the gene transcription. Additionally, inhibition of BRD4 impairs the HIF-1α stabilization, downregulating the expression of hypoxia-induced genes. Results from whole-genome gene expression assays after stable knockdown of XBP1 and ATF4 reveal that most (86%) of the UPR genes regulated by BET proteins are dependent of XBP1 and only 32% by ATF4. Moreover, almost all genes regulated by ATF4 are also XBP1-dependent. This result may be due to the fact that ATF4 regulates IRE1α expression and thus modulates the XBP1 mRNA splicing. Administration of JQ1 in an IRI model supports that blockage of BRD4 ameliorates the renal damage (reducing BUN and creatinine levels) due to a decreased UPR activation and expression of HIF-1α target genes. As consequence, the expression of inflammatory genes and the inflammatory cell infiltration is diminished. Conclusion Our results show that BRD4 protein regulates two key processes, induction of HIF-1α transcription factor and UPR pathway activation triggered by renal hypoxia. Pharmacological inhibition of BET proteins reduces the activation these pathways, ameliorating renal damage and avoiding its progression.

scholarly journals Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 372 ◽  
Author(s):  
Delasa Aghamirzaie ◽  
Karthik Raja Velmurugan ◽  
Shuchi Wu ◽  
Doaa Altarawy ◽  
Lenwood S. Heath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Data Sets ◽  
Motif Analysis ◽  
Chromatin Immunoprecipitation Sequencing

Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user’s gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/

scholarly journals The Herbal Cocktail GSYJ Attenuated Airway Inflammatory Cell Infiltration in a Chronic Asthmatic Mouse Model

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Chung-Jen Chiang ◽  
Shu-Lun Chang ◽  
Li-Jen Lin
Keyword(s):  
Transcription Factors ◽  
Mouse Model ◽  
Inflammatory Cell ◽  
Expression Profiles ◽  
Lavage Fluid ◽  
Inflammatory Cell Infiltration ◽  
Cell Infiltration ◽  
Chronic Asthma ◽  
Total Ige ◽  
Expression Of Genes

This study explored the potential therapeutic efficacy of GSYJ in attenuating asthma symptom severity and aimed to determine the immunomodulatory mechanism of GSYJ. A mouse model of chronic asthma induced by repeated Dermatophagoides pteronyssinus (Der p) challenge was established. In addition, 30 minutes before Der p challenge, the mice were orally administered GSYJ (1 g/kg). The mice were sacrificed to evaluate inflammatory cell infiltration, collagen deposition in the lung, total IgE in serum, and expression profiles of various cytokines in bronchoalveolar lavage fluid (BALF) and various genes in lung tissue. Furthermore, 30 minutes after the addition of GSYJ to RAW264.7 cell cultures, 100 ng/ml LPS was added to evaluate the effect of the drug on the LPS-induced expression of genes, proteins, and transcription factors. GSYJ may regulate transcription factors (cJUN/IRF3/NF-κB) to decrease the expression of IL-1β, IL-6, RANTES, and iNOS in macrophages and affect the IL-12, IFN-γ, IL-5, and IL-6 levels in the BALF of mice to relieve asthma symptoms, such as inflammatory cell infiltration, hyperresponsiveness, and increased serum total IgE levels. Therefore, GSYJ has the potential to be developed into a drug treatment for chronic asthma.

scholarly journals Chemokine Expression Precedes Inflammatory Cell Infiltration and Chemokine Receptor and Cytokine Expression during the Initiation of Murine Lupus Nephritis

2001 ◽  
Vol 12 (7) ◽  
pp. 1369-1382 ◽  
Author(s):  
GUILLERMO PÉREZ DE LEMA ◽  
HOLGER MAIER ◽  
ELENA NIETO ◽  
VOLKER VIELHAUER ◽  
BRUNO LUCKOW ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Proinflammatory Cytokines ◽  
Chemokine Receptor ◽  
Chemokine Receptors ◽  
Renal Damage ◽  
Inflammatory Cell ◽  
Inflammatory Cell Infiltration ◽  
Cell Infiltration ◽  
Mononuclear Cell Infiltration ◽  
Monocyte Chemoattractant Protein 1

Abstract. Lupus nephritis is characterized by immune complex deposition and inflammatory cell infiltration. Therefore, the initiation and progression of lupus nephritis in MRL/MpJ Faslpr/lpr(MRL/lpr) mice were investigated, with a focus on the expression of several chemokines and chemokine receptors. Mice were monitored for proteinuria from 6 to 20 wk of age, and kidneys were examined every 2 wk by light microscopy, electron microscopy, and immunohistologic analyses. Furthermore, the expression of chemokines, chemokine receptors, and proinflammatory cytokines was analyzed in ribonuclease protection assays. MRL/lpr mice demonstrated increased expression of monocyte chemoattractant protein-1, regulated upon activation, normal T cell-expressed and -secreted protein, inducible protein of 10 kD, and macrophage inflammatory protein-1β at week 8. At that time point, levels of circulating and glomerular immune complexes were increased, and no proteinuria or histopathologic signs of renal damage could be observed. As assessed in immunohistochemical andin situhybridization analyses, monocyte chemoattractant protein-1 and regulated upon activation, normal T cell-expressed and -secreted protein expression was preferentially located in the glomeruli and interstitium. Mononuclear cell infiltration of the kidney was observed by weeks 10 to 12. At week 12, the renal expression of chemokine receptor 1 (CCR1), CCR2, and CCR5 was increased, mice became proteinuric, and renal damage was histologically evident. Finally, the expression of proinflammatory cytokines was detected (weeks 12 to 14). In summary, (1) chemokines are upregulated before inflammatory cell infiltration, proteinuria, and kidney damage are observed; (2) chemokine generation is restricted to sites of subsequent inflammatory cell infiltration,i.e., glomeruli and interstitium; (3) chemokine receptor expression parallels mononuclear cell infiltration; and (4) proinflammatory cytokines are upregulated later, in parallel with inflammatory cell infiltration and the onset of proteinuria. These results support the hypothesis that chemokines initiate leukocyte infiltration and precede proteinuria and renal damage in MRL/lpr mice.

scholarly journals KLF3 Represses the Inflammatory Response in Macrophages

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 36-36
Author(s):  
Jessica M Salmon ◽  
Casie Leigh Reed ◽  
Maddyson Bender ◽  
Helen Lorraine Mitchell ◽  
Vanessa Fox ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Time Course ◽  
Target Genes ◽  
Wild Type ◽  
Cell Counts ◽  
Inflammatory Macrophages

Krüppel-like factors (KLFs) are a family of transcription factors that play essential roles in the development and differentiation of the hematopoietic system. These transcription factors possess highly conserved C-terminal zinc-finger motifs, which enable their binding to GC-rich, or CACC-box, motifs in promoter and enhancer regions of target genes. The N-terminal domains of these proteins are more varied and mediate the recruitment of various co-factors, which can form a complex with either activator or repressor function. Acting primarily as a gene repressor through its recruitment of CtBPs and histone deacetylases (HDACs) [1], we have recently shown that KLF3 competes with KLF1 bound sites in the genome to repress gene expression during erythropoiesis [2]. However, the function of Klf3 in other lineages has been less well studied. This widely expressed transcription factor has reported roles in the differentiation of marginal zone B cells, eosinophil function and inflammation [3]. We utilised the Klf3-null mouse model [4] to more closely examine the role of Klf3 in innate inflammatory cells. These mice exhibit elevated white cell counts, including monocytes (Figure 1A), and inflammation of the skin. Conditional knockout of Klf4 in myeloid cells leads to a deficiency of inflammatory macrophages [5]. To test our hypothesis KLF3 normally represses inflammation, perhaps by antagonising the action of KLF4, bone-marrow derived macrophages (BMDM) were generated from wild-type or Klf3-null mice and stimulated with the bacterial toxin lipopolysaccharide (LPS). In wild type BMDM, LPS induces Klf3 gene expression and activation then delayed repression of target genes such as Lgals3 (galectin-3) over a 21 hour time course (Figure 1B). Quantitative real-time PCR and mRNA-seq of WT v Klf3-null macrophages identified ~100 differentially expressed genes involved in proliferation, macrophage activation and inflammation. We transduced the monocyte cell line, RAW264.7 (that expresses Klf4, Klf3 and Klf2), with a retroviral vector expressing a tamoxifen-inducible KLF3-ER fusion construct. KLF3 induced cell cycle arrest and macrophage differentiation. We will report on KLF3-induced gene expression changes (repression and activation), and ChIP-seq for KLF3, in RAW cells. The results shed light on the mechanism by which KLF3 normally represses monocyte/macrophage responses to infection. This study highlights the importance of key transcriptional regulators that tightly control gene expression during inflammation. Loss of Klf3 leads to alterations in this process, resulting in hyper-activation of inflammatory macrophages, increased white cell counts and inflammation of the skin. A greater knowledge of the inflammatory process and how it is regulated is important for our understanding of acute infection and inflammatory disease. Further studies are planned to investigate the role of the KLF3 transcription factor in response to inflammation in vivo. References: 1. Pearson, R., et al., Kruppel-like transcription factors: A functional family. Int J Biochem Cell Biol, 2007. W2. Ilsley, M.D., et al., Kruppel-like factors compete for promoters and enhancers to fine-tune transcription. Nucleic Acids Res, 2017. 45(11): p. 6572-6588. W3. Knights, A.J., et al., Kruppel-like factor 3 (KLF3) suppresses NF-kappaB-driven inflammation in mice. J Biol Chem, 2020. 295(18): p. 6080-6091. W4. Sue, N., et al., Targeted disruption of the basic Kruppel-like factor gene (Klf3) reveals a role in adipogenesis. Mol Cell Biol, 2008. 28(12): p. 3967-78. W5. Alder, J.K., et al., Kruppel-like factor 4 is essential for inflammatory monocyte differentiation in vivo. J Immunol, 2008. 180(8): p. 5645-52. Figure 1: Elevated WCC (A) and inflammatory markers (B) in BMDM after LPS stimulation. 1. Total WCC in adult mice (3-6 months old) of the indicated genotypes. There is a statistically significant increase in the WCC in Klf3-/- v wild type mice (P<0.001 by student's t test). B. Time course (hours) after LPS stimulation of confluent BMDM. Klf3 is induced 3-fold by LPS and KLF3-target genes such as Lgals3 are not fully repressed by 21 hours in knockout mice. Figure 1 Disclosures Perkins: Novartis Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees.

scholarly journals Identification of Deregulated Transcription Factors Involved in Specific Bladder Cancer Subtypes

10.29007/v7qj ◽  
2020 ◽  
Author(s):  
Magali Champion ◽  
Julien Chiquet ◽  
Pierre Neuvial ◽  
Mohamed Elati ◽  
François Radvanyi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
The Cancer Genome Atlas ◽  
Reference Network ◽  
Data Set ◽  
Cancer Subtypes ◽  
Cancer Data

Comparison between tumoral and healthy cells may reveal abnormal regulation behaviors between a transcription factor and the genes it regulates, without exhibiting differential expression of the former genes. We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription factors to their downstream targets using gene expression data. Gene expression levels in tumor samples are then carefully compared to this reference network to detect deregulated target genes. A linear model is finally used to measure the ability of each transcription factor to explain these deregulations. We assess the performance of our method by numerical experiments on a public bladder cancer data set derived from the Cancer Genome Atlas project. We identify genes known for their implication in the development of specific bladder cancer subtypes as well as new potential biomarkers.

Estrogen receptor action through target genes with classical and alternative response elements

2003 ◽  
Vol 75 (11-12) ◽  
pp. 1757-1769 ◽  
Author(s):  
P. J. Kushner ◽  
P. Webb ◽  
R. M. Uht ◽  
M.-M. Liu ◽  
R. H. Price
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
Cell Types ◽  
Binding Domain ◽  
Environmental Estrogens ◽  
Alternative Response ◽  
Promoter Elements ◽  
Response Elements

The estrogen receptors alpha and beta (ERα and ERβ) mediate the changes in gene expression from physiological and environmental estrogens. Early studies identified classical estrogen response elements (EREs) in the promoter region of target genes whose expression is regulated by estrogen and to which the ERs bind via their DNA-binding domain (DBD). EREs in the pituitary prolactin promoter, for example, mediate an activation by both ERα and ERβ albeit with different affinities for different ligands. Full activation in most cell types requires the integrity of the activation function 2 (AF-2) in the receptors ligand binding domain (LBD), which is engaged by estrogens and disengaged by tamoxifen, raloxifene, and other antiestrogens. However, in some cells and ERE contexts, the AF-1 in the ERα amino terminal domain (NTD) is sufficient. We now know that ERs also regulate expression of target genes that do not have EREs, but instead have various kinds of alternative response elements that bind heterologous transcription factors whose activity is regulated by interactions with ERs. Thus, ERα activates genes, including collagenase and cyclin D1, an important mediator of cellular proliferation, by AP-1 and CRE sites, which bind Jun/Fos or Jun/ATF-2 transcription factors. ERα also activates gene expression through GC-rich elements that bind the SP1 transcription factor. Finally, we also know that ERs mediate inhibition of the expression of many genes. In one well-studied instance, ERs counterexpression of genes involved in the inflammatory response by inhibiting the action at tumor necrosis factor response elements (TNF-REs) that bind the NFkappaB transcription factor. ERβ is especially efficient at this inhibition. ERα activation of AP-1/CRE target genes is of special interest because of the putative role of these target genes in mediating proliferation. The AF-1 and AF-2 functions of ERα are both needed for this activation in most cell types. However, in uterine cells, the AF-1 function is sufficient. Thus, the antiestrogen tamoxifen, which allows AF-1, mimics estrogen and drives activation of AP-1/CRE target genes and proliferation of uterine cells. This estrogen-like action, which can increase the risk of uterine cancer, complicates the use of tamoxifen to prevent breast cancer. Surprisingly, ERβ inhibits AP-1/CRE target genes in the presence of estrogen. When both receptors are present, ERβ efficiently opposes activation by ERα. Moreover, ERβ activates the AP-1/CRE target genes in the presence of antiestrogens especially so-called "complete" antiestrogens raloxifene, and ICI 182, 780. We here review the evidence for different kinds of promoter elements that mediate ER action, for the differential ligand preferences of ERα and ERβ at these different elements, and the potential mechanisms by which they are mediated. One attractive strategy for the investigation and comparison of potential environmental estrogens is to assay their activity in cell culture systems using reporter genes with simplified promoter elements. Thus, the findings of complexity in ERα and ERβ activation at different types of response elements needs to be taken into account in the development and interpretation of assays using simplified promoter elements systems.

scholarly journals Micro RNA Targeted Transcription Factors for Fruit Quality Improvement

2008 ◽  
Author(s):  
Tzahi Arazi ◽  
Vivian Irish ◽  
Asaph Aharoni
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Fruit Development ◽  
Target Genes ◽  
Tomato Fruit ◽  
Fleshy Fruit ◽  
Green Fruit ◽  
Transcription Factor Target ◽  
Ripening Mutants

Fruits are unique to flowering plants and represent an important component of human and animal diets. Development and maturation of tomato fruit is a well-programmed process, and yet, only a limited number of factors involved in its regulation have been characterized. Micro-RNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in animals and plants. Plant miRNAs have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators, especially transcription factors. Recently, we and others have demonstrated that miRNAs and other type of small RNAs are expressed in tomato fruit, and target putative transcription factors during its development and maturation. The original objectives of the approved proposal were: 1. To identify fruit miRNA transcription factor target genes through a bioinformatic approach. 2. To identify fruit miRNA transcription factor target genes up-regulated in tomato Dicer-like 1 silenced fruit. 3. To establish the biological functions of selected transcription factors and examine their utility for improving fleshy fruit quality trait. This project was approved by BARD as a feasibility study to allow initial experiments to peruse objective 2 as described above in order to provide initial evidence that miRNAs do play a role in fruit development. The approach planned to achieve objective 2, namely to identify miRNA transcription factor targets was to clone and silence the expression of a tomato DCL1 homolog in different stages of fruit development and examine alterations to gene expression in such a fruit in order to identify pathways and target genes that are regulated by miRNA via DCL1. In parallel, we characterized two transcription factors that are regulated by miRNAs in the fruit. We report here on the cloning of tomato DCL1 homolog, characterization of its expression in fruit flesh and peel of wild type and ripening mutants and generation of transgenic plants that silence SlDCL1 specifically in the fruit. Our results suggest that the tomato homolog of DCL1, which is the major plant enzyme involved in miRNA biogenesis, is present in fruit flesh and peel and differentially expressed during various stages of fruit development. In addition, its expression is altered in ripening mutants. We also report on the cloning and expression analysis of Sl_SBP and Sl_ARF transcription factors, which serve as targets of miR157 and miR160, respectively. Our data suggest that Sl_SBP levels are highest during fruit ripening supporting a role for this gene in that process. On the other hand Sl_ARF is strongly expressed in green fruit up to breaker indicating a role for that gene at preripening stage which is consistent with preliminary in_situ analyses that suggest expression in ovules of immature green fruit. The results of this feasibility study together with our previous results that miRNAs are expressed in the fruit indeed provide initial evidence that these regulators and their targets play roles in fruit development and ripening. These genes are expected to provide novel means for genetic improvement of tomato fleshy fruit.  

scholarly journals midline represses Dpp signaling and target gene expression in Drosophila ventral leg development

2021 ◽  
Author(s):  
Lindsay A. Phillips ◽  
Markle L. Atienza ◽  
Jae-Ryeon Ryu ◽  
Pia C. Svendsen ◽  
Lynn K. Kelemen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Sequence ◽  
Target Gene ◽  
Target Genes ◽  
T Box ◽  
Leg Development ◽  
Summary Statement

AbstractVentral leg patterning in Drosophila is controlled by the expression of the redundant T-box Transcription factors midline (mid) and H15. Here we show that mid represses the Dpp-activated gene Daughters against decapentaplegic (Dad) through a consensus TBE site in the minimal enhancer, Dad13. Mutating the Dad13 DNA sequence results in an increased and broadening of Dad expression. We further demonstrate that the engrailed-homology-1 domain of Mid is critical for regulating the levels of phospho-Mad, a transducer of Dpp-signaling. However, we find that mid does not affect all Dpp-target genes as we demonstrate that brinker (brk) expression is unresponsive to mid. This study further illuminates the interplay between mechanisms involved in determination of cellular fate and the varied roles of mid.Summary statementVentral patterning is controlled in part by the T-box Transcription factor midline blocking Dpp signaling and Dpp-activated genes, though midline does not affect the Dpp-repressed gene brk.

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