scholarly journals A Central Role for Canonical PRC1 in Shaping the 3D Nuclear Landscape

2019 ◽  
Author(s):  
Shelagh Boyle ◽  
Ilya M. Flyamer ◽  
Iain Williamson ◽  
Dipta Sengupta ◽  
Wendy A. Bickmore ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Gene Activation ◽  
Embryonic Stem ◽  
Nuclear Architecture ◽  
Regulatory System ◽  
Spatial Arrangement ◽  
Polycomb Group ◽  
List Type

AbstractPolycomb group (PcG) proteins silence gene expression by chemically and physically modifying chromatin. A subset of PcG target loci are compacted and cluster in the nucleus to form observable bodies; a conformation which is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organisation and their relationship with transcription remains poorly understood. Here we examine the role of Polycomb Repressive Complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells (mESCs). Using a combination of imaging and Hi-C analyses we show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale. Impairment of PRC1 enzymatic activity does not directly disrupt these interactions. We demonstrate that PcG targets coalesce in vivo, and that developmentally induced expression of one of the target loci disrupts this spatial arrangement. Finally, we show that transcriptional activation and the loss of PRC1-mediated interactions are seperable events. These findings provide important insights into the function of PRC1, whilst highlighting the complexity of this regulatory system.HighlightsLoss of RING1B substantially disrupts nuclear architecture.PRC1 mediated looping can occur at a Mb scale and is independent of CTCF.Polycomb mediated looping is driven by canonical PRC1 complexes.Multimeric PRC1-mediated interactions occur in vitro and in vivo.Disruption of PRC1-mediated looping is independent of gene activation.

Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

2005 ◽  
Vol 83 (4) ◽  
pp. 535-547 ◽  
Author(s):  
Gareth N Corry ◽  
D Alan Underhill
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Nuclear Architecture ◽  
Subnuclear Localization ◽  
Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

Histone deacetylase–mediated transcriptional activation reduces proviral loads in HTLV-1–associated myelopathy/tropical spastic paraparesis patients

Blood ◽  
2007 ◽  
Vol 110 (10) ◽  
pp. 3722-3728 ◽  
Author(s):  
Agnès Lezin ◽  
Nicolas Gillet ◽  
Stéphane Olindo ◽  
Aïssatou Signaté ◽  
Nathalie Grandvaux ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Transcriptional Activation ◽  
Gene Activation ◽  
Spastic Paraparesis ◽  
Viral Gene Expression ◽  
Tropical Spastic Paraparesis ◽  
Viral Reservoir ◽  
Viral Gene

AbstractEpigenetic modifications of chromatin may play a role in maintaining viral latency and thus persistence of the human T-lymphotropic virus type 1 (HTLV-1), which is responsible for HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP). A major determinant of disease progression is increased peripheral blood proviral load (PVL), possibly via the accumulation of infected cells in the central nervous system (CNS) creating a damaging inflammatory response. Current therapeutic approaches that focus on reducing either cell proliferation, viral replication, or tissue invasion are still unsatisfactory. Contrasting with these inhibitory strategies, we evaluated the efficacy of a novel approach aimed, paradoxically, at activating viral gene expression to expose virus-positive cells to the host immune response. We used valproate (VPA), a histone deacetylase inhibitor that has been used for decades as a chronic, safe treatment for epileptic disorders. Based on in vitro and in vivo data, we provide evidence that transient activation of the latent viral reservoir causes its collapse, a process that may alleviate the condition of HAM/TSP. This represents the first such approach to treating HAM/TSP, using gene activation therapy to tilt the host-pathogen balance in favor of an existing antiviral response. This trial is registered at http://clinicaltrials.gov/as no. NCT00519181.

scholarly journals In Vivo Requirement of Activator-Specific Binding Targets of Mediator

2000 ◽  
Vol 20 (23) ◽  
pp. 8709-8719 ◽  
Author(s):  
Jin Mo Park ◽  
Hye-Suk Kim ◽  
Sang Jun Han ◽  
Moon-Sun Hwang ◽  
Young Chul Lee ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Specific Binding ◽  
Gene Activation ◽  
Dna Interaction ◽  
Activation Process ◽  
Binding Region ◽  
Physiological Conditions ◽  
Functional Analyses

ABSTRACT There has been no unequivocal demonstration that the activator binding targets identified in vitro play a key role in transcriptional activation in vivo. To examine whether activator-Mediator interactions are required for gene transcription under physiological conditions, we performed functional analyses with Mediator components that interact specifically with natural yeast activators. Different activators interact with Mediator via distinct binding targets. Deletion of a distinct activator binding region of Mediator completely compromised gene activation in vivo by some, but not all, transcriptional activators. These demonstrate that the activator-specific targets in Mediator are essential for transcriptional activation in living cells, but their requirement was affected by the nature of the activator-DNA interaction and the existence of a postrecruitment activation process.

Butyrate induces selective transcriptional activation of a hypomethylated embryonic globin gene in adult erythroid cells

Blood ◽  
1988 ◽  
Vol 72 (5) ◽  
pp. 1536-1542
Author(s):  
LJ Burns ◽  
JG Glauber ◽  
GD Ginder
Keyword(s):  
Sodium Butyrate ◽  
Transcriptional Activation ◽  
Globin Gene ◽  
Gene Activation ◽  
Globin Genes ◽  
Erythroid Cells ◽  
Hemoglobin Switching ◽  
High Level

An animal model of hemoglobin switching has been developed in which anemic adult chickens are treated with 5-azacytidine and sodium butyrate or alpha-aminobutyric acid, thereby resulting in activation of the embryonic rho-globin gene in adult erythroid cells. In vitro nuclear runoff transcription assays using erythroid nuclei from treated birds show that the mechanism of activation of the rho-globin gene is transcriptional whereas no transcriptional activation of the embryonic epsilon-globin gene occurs. The action of 5-azacytidine appears to be as an inhibitor of DNA methylation because other S-phase active cytotoxic drugs, when substituted for 5-azacytidine, do not cause demethylation of the embryonic globin genes, nor do they allow transcriptional activation to occur. Embryonic rho-globin gene activation in this model is not due to selection of primitive erythroid cells since a subpopulation of primitive erythroid cells is not evident either morphologically or when cells are probed for embryonic and adult globin RNA by in situ hybridization. These studies show that demethylation by 5-azacytidine is a prerequisite but not sufficient cis- regulatory event for a high level of transcriptional activation of the embryonic rho-globin gene in adult erythroid cells in vivo. The possible basis for the selective transcriptional activation by sodium butyrate in this system is discussed.

scholarly journals circRNA_0046367 Prevents Hepatoxicity of Lipid Peroxidation: An Inhibitory Role against Hepatic Steatosis

2017 ◽  
Vol 2017 ◽  
pp. 1-16 ◽  
Author(s):  
Xing-Ya Guo ◽  
Jian-Neng Chen ◽  
Fang Sun ◽  
Yu-Qin Wang ◽  
Qin Pan ◽  
...  
Keyword(s):  
Lipid Peroxidation ◽  
Hepatic Steatosis ◽  
Transcriptional Activation ◽  
Regulatory System ◽  
Inhibitory Effect ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Triglyceride Accumulation

Hepatic steatosis reflects the miRNA-related pathological disorder with triglyceride accumulation and lipid peroxidation, which leads to nonalcoholic steatohepatitis, liver fibrosis/cirrhosis, and even hepatocellular carcinoma. Circular RNA (circRNA)/miRNA interaction reveals a novel layer of epigenetic regulation, yet the miRNA-targeting circRNA remains uncertain in hepatic steatosis. Here, we uncover circRNA_0046367 to be endogenous modulator of miR-34a that underlies hepatic steatosis. In contrast to its expression loss during the hepatocellular steatosis in vivo and in vitro, circRNA_0046367 normalization abolished miR-34a’s inhibitory effect on peroxisome proliferator-activated receptorα(PPARα) via blocking the miRNA/mRNA interaction with miRNA response elements (MREs). PPARαrestoration led to the transcriptional activation of genes associated with lipid metabolism, including carnitine palmitoyltransferase 2 (CPT2) and acyl-CoA binding domain containing 3 (ACBD3), and then resulted in the steatosis resolution. Hepatotoxicity of steatosis-related lipid peroxidation, being characterized by mitochondrial dysfunction, growth arrest, and apoptosis, is resultantly prevented after the circRNA_0046367 administration. These findings indicate a circRNA_0046367/miR-34a/PPARαregulatory system underlying hepatic steatosis. Normalized expression of circRNA_0046367 may ameliorate the lipoxidative stress on the basis of steatosis attenuation. circRNA_0046367, therefore, is suggested to be potential approach to the therapy of lipid peroxidative damage.

scholarly journals EGFR confers exquisite specificity of Wnt9a-Fzd9b signaling in hematopoietic stem cell development

2018 ◽  
Author(s):  
Stephanie Grainger ◽  
Nicole Nguyen ◽  
Jenna Richter ◽  
Jordan Setayesh ◽  
Brianna Lonquich ◽  
...  
Keyword(s):  
Stem Cell ◽  
Wnt Signaling ◽  
Hematopoietic Stem Cell ◽  
Cell Biology ◽  
Embryonic Stem ◽  
Cell Development ◽  
List Type ◽  
Hematopoietic Stem

SummaryThe mechanisms of Wnt-Frizzled (Fzd) signaling selectivity and their biological implications remain unclear. We demonstrate for the first time that the epidermal growth factor receptor (EGFR) is required as a co-factor for Wnt signaling. Using genetic studies in zebrafish, paired within vitrocell biology and biochemistry, we have determined that Fzd9b signals specifically with Wnt9ain vivoandin vitroto elicit β-catenin dependent Wnt signals that regulate hematopoietic stem and progenitor cell (HSPC) development in the dorsal aorta. This requirement is conserved in the derivation of HSPCs from human embryonic stem cells. Wnt9a-Fzd9b specificity requires two intracellular domains in Fzd9b, which interact with EGFR as a required co-factor to promote signal transduction. EGFR phosphorylates one tyrosine residue on Fzd9b, a requirement for the Wnt signal. These findings indicate that Wnt signaling interactions can be exquisitely specific and inform protocols for derivation of HSPCsin vitro.HighlightsAnin vitrosignaling screen identifies Fzd9b as a Wnt9a-specific receptor.Fzd9b and Wnt9a regulate hematopoietic stem cell development as a cognate pair.WNT9A and FZD9 are required for HSPC derivation from human pluripotent cellsin vitro.EGFR confers specificity to Wnt9a-Fzd9b signaling in zebrafish and human cells.

scholarly journals Transcriptional Activation by Bacillus subtilis ResD: Tandem Binding to Target Elements and Phosphorylation-Dependent and -Independent Transcriptional Activation

2004 ◽  
Vol 186 (7) ◽  
pp. 2028-2037 ◽  
Author(s):  
Hao Geng ◽  
Shunji Nakano ◽  
Michiko M. Nakano
Keyword(s):  
Bacillus Subtilis ◽  
Transcriptional Activation ◽  
Response Regulator ◽  
Gene Activation ◽  
Phosphorylation Site ◽  
Oxygen Limitation ◽  
Nitrate Respiration ◽  
Expression Of Genes

ABSTRACT The expression of genes involved in nitrate respiration in Bacillus subtilis is regulated by the ResD-ResE two-component signal transduction system. The membrane-bound ResE sensor kinase perceives a redox-related signal(s) and phosphorylates the cognate response regulator ResD, which enables interaction of ResD with ResD-dependent promoters to activate transcription. Hydroxyl radical footprinting analysis revealed that ResD tandemly binds to the −41 to −83 region of hmp and the −46 to −92 region of nasD. In vitro runoff transcription experiments showed that ResD is necessary and sufficient to activate transcription of the ResDE regulon. Although phosphorylation of ResD by ResE kinase greatly stimulated transcription, unphosphorylated ResD, as well as ResD with a phosphorylation site (Asp57) mutation, was able to activate transcription at a low level. The D57A mutant was shown to retain the activity in vivo to induce transcription of the ResDE regulon in response to oxygen limitation, suggesting that ResD itself, in addition to its activation through phosphorylation-mediated conformation change, senses oxygen limitation via an unknown mechanism leading to anaerobic gene activation.

scholarly journals Butyrate induces selective transcriptional activation of a hypomethylated embryonic globin gene in adult erythroid cells

Blood ◽  
1988 ◽  
Vol 72 (5) ◽  
pp. 1536-1542 ◽  
Author(s):  
LJ Burns ◽  
JG Glauber ◽  
GD Ginder
Keyword(s):  
Sodium Butyrate ◽  
Transcriptional Activation ◽  
Globin Gene ◽  
Gene Activation ◽  
Globin Genes ◽  
Erythroid Cells ◽  
Hemoglobin Switching ◽  
High Level

Abstract An animal model of hemoglobin switching has been developed in which anemic adult chickens are treated with 5-azacytidine and sodium butyrate or alpha-aminobutyric acid, thereby resulting in activation of the embryonic rho-globin gene in adult erythroid cells. In vitro nuclear runoff transcription assays using erythroid nuclei from treated birds show that the mechanism of activation of the rho-globin gene is transcriptional whereas no transcriptional activation of the embryonic epsilon-globin gene occurs. The action of 5-azacytidine appears to be as an inhibitor of DNA methylation because other S-phase active cytotoxic drugs, when substituted for 5-azacytidine, do not cause demethylation of the embryonic globin genes, nor do they allow transcriptional activation to occur. Embryonic rho-globin gene activation in this model is not due to selection of primitive erythroid cells since a subpopulation of primitive erythroid cells is not evident either morphologically or when cells are probed for embryonic and adult globin RNA by in situ hybridization. These studies show that demethylation by 5-azacytidine is a prerequisite but not sufficient cis- regulatory event for a high level of transcriptional activation of the embryonic rho-globin gene in adult erythroid cells in vivo. The possible basis for the selective transcriptional activation by sodium butyrate in this system is discussed.

scholarly journals An Improved Recombination-BasedIn VivoExpression Technology-Like Reporter System Reveals DifferentialcyaAGene Activation in Bordetella Species

2013 ◽  
Vol 81 (4) ◽  
pp. 1295-1305 ◽  
Author(s):  
Matthew S. Byrd ◽  
Eliza Mason ◽  
Michael W. Henderson ◽  
Erich V. Scheller ◽  
Peggy A. Cotter
Keyword(s):  
Virulence Factors ◽  
Gene Activation ◽  
Regulatory System ◽  
Reporter System ◽  
Fluorescent Reporter ◽  
Content Type ◽  
Genes Encoding ◽  
Species Specific

ABSTRACTBordetella pertussisandBordetella bronchisepticarely on the global two-component regulatory system BvgAS to control expression of distinct phenotypic phases. In the Bvg−phase, expression ofvrggenes, including those required for motility inB. bronchiseptica, is activated and genes encoding virulence factors are not expressed. Conversely, in the Bvg+phase, genes encoding virulence factors are highly expressed while genes necessary for motility are repressed. Although several genetic analyses have demonstrated the importance of the Bvg+phase during respiratory infection, Bvg-regulated gene activation inB. bronchisepticahas not been investigatedin vivo. To address this, we developed a plasmid, pGFLIP, that encodes a sensitive Flp recombinase-based fluorescent reporter system able to document gene activation bothin vitroandin vivo. Using pGFLIP, we demonstrated thatcyaA, considered to be a “late” Bvg+phase gene, is activated substantially earlier inB. bronchisepticathanB. pertussisfollowing a switch from Bvg−to Bvg+phase conditions. We show that the altered activation ofcyaAis not due to differences in thecyaApromoter or in thebvgASalleles ofB. bronchisepticacompared toB. pertussis, but appears to be species specific. Finally, we used pGFLIP to show thatflaAremains repressed during infection, confirming thatB. bronchisepticadoes not modulate to the Bvg−phasein vivo.

scholarly journals Synthetic Maturation of Multilineage Human Liver Organoids via Genetically Guided Engineering

2020 ◽  
Author(s):  
Jeremy J. Velazquez ◽  
Ryan LeGraw ◽  
Farzaneh Moghadam ◽  
Yuqi Tan ◽  
Jacquelyn Kilbourne ◽  
...  
Keyword(s):  
Single Cell ◽  
Transcriptional Activation ◽  
Computational Analysis ◽  
Therapeutic Potential ◽  
Fetal Liver ◽  
List Type ◽  
Native Liver ◽  
Liver Organoids

SUMMARYPluripotent stem cell (PSC)-derived organoids are emerging as novel human-based microphysiological models but display immature phenotypes with limited subsets of endothelial or stromal cells. Here we demonstrate that in vitro manipulation of gene regulatory networks (GRNs) in PSC-derived liver organoids selected either through computational analysis or targeted tissue design can advance tissue maturation in vitro. Through an unbiased comparison with the genetic signature of mature livers, we identify downregulated GRNs in fetal liver organoids compared to adult livers. We demonstrate that overexpression of PROX1 and ATF5, together with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, drives maturation in vitro. Single cell analyses reveal hepatobiliary-, endothelial-, and stellate-like cell populations. The engineered organoids demonstrate enhanced vasculogenesis, capture native liver characteristics (e.g. FXR signaling, CYP3A4 activity), and exhibit therapeutic potential in mice. Collectively, our approach provides a genetically guided framework for engineering developmentally advanced multilineage tissues from hiPSCs.HIGHLIGHTSIn vitro tissue maturation via genetically encoded molecular programsComputational analysis to identify maturation transcription factors in liver organoidsPromoting vascularization of organoids via genetically encoded molecular programsSingle cell analysis of parenchymal and non-parenchymal cellsModeling of native liver functions and in vivo therapeutic potentialGraphical Abstract

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