scholarly journals Concerted localization-resets precede YAP-dependent transcription

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
J. Matthew Franklin ◽  
Rajarshi P. Ghosh ◽  
Quanming Shi ◽  
Michael P. Reddick ◽  
Jan T. Liphardt
Keyword(s):  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Size Control ◽  
Nucleocytoplasmic Shuttling ◽  
Cell Localization ◽  
Actomyosin Contractility ◽  
Real Time Visualization ◽  
Transformed Cell Lines ◽  
Target Gene Transcription

Abstract Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using advanced tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus (“localization-resets”) activates YAP target genes. These “resets” are induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we show a strict association between these resets and downstream transcription. Oncogenically-transformed cell lines lack localization-resets and instead show dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.

scholarly journals Concerted localization-resets precede YAP-dependent transcription

2019 ◽  
Author(s):  
Rajarshi P. Ghosh ◽  
J. Matthew Franklin ◽  
Quanming Shi ◽  
Michael P. Reddick ◽  
Jan T. Liphardt
Keyword(s):  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Size Control ◽  
Nucleocytoplasmic Shuttling ◽  
Cell Localization ◽  
Actomyosin Contractility ◽  
Real Time Visualization ◽  
Transformed Cell Lines ◽  
Target Gene Transcription

Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using new tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus (“localization-resets”) activates YAP target genes. These “resets” could be induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we observed a strict association between these resets and downstream transcription. Oncogenically-transformed transformed cell lines lacked localization-resets and instead showed dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a new model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.

scholarly journals Mutant Alleles of the Drosophila trithorax Gene Produce Common and Unusual Homeotic and Other Developmental Phenotypes

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 319-344
Author(s):  
Thomas R Breen
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Protein Isoforms ◽  
Homeotic Genes ◽  
Set Domain ◽  
Human Homologue ◽  
Terminal Set ◽  
Hypomorphic Alleles ◽  
Different Levels ◽  
Target Gene Transcription

Abstract trithorax (trx) encodes chromosome-binding proteins required throughout embryogenesis and imaginal development for tissue- and cell-specific levels of transcription of many genes including homeotic genes of the ANT-C and BX-C. trx encodes two protein isoforms that contain conserved motifs including a C-terminal SET domain, central PHD fingers, an N-terminal DNA-binding homology, and two short motifs also found in the TRX human homologue, ALL1. As a first step to characterizing specific developmental functions of TRX, I examined phenotypes of 420 combinations of 21 trx alleles. Among these are 8 hypomorphic alleles that are sufficient for embryogenesis but provide different levels of trx function at homeotic genes in imaginal cells. One allele alters the N terminus of TRX, which severely impairs larval and imaginal growth. Hypomorphic alleles that alter different regions of TRX equivalently reduce function at affected genes, suggesting TRX interacts with common factors at different target genes. All hypomorphic alleles examined complement one another, suggesting cooperative TRX function at target genes. Comparative effects of hypomorphic genotypes support previous findings that TRX has tissue-specific interactions with other factors at each target gene. Some hypomorphic genotypes also produce phenotypes that suggest TRX may be a component of signal transduction pathways that provide tissue- and cell-specific levels of target gene transcription.

scholarly journals PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes

PPAR Research ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Li Fang ◽  
Man Zhang ◽  
Yanhui Li ◽  
Yan Liu ◽  
Qinghua Cui ◽  
...  
Keyword(s):  
In Silico ◽  
Target Gene ◽  
Target Genes ◽  
Prediction Method ◽  
Peroxisome Proliferator ◽  
Physiological Processes ◽  
Peroxisome Proliferator Activated Receptors ◽  
High Throughput Gene Expression ◽  
Responsive Element ◽  
Target Gene Transcription

The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors of the nuclear receptor superfamily. Upon ligand binding, PPARs activate target gene transcription and regulate a variety of important physiological processes such as lipid metabolism, inflammation, and wound healing. Here, we describe the first database of PPAR target genes, PPARgene. Among the 225 experimentally verified PPAR target genes, 83 are for PPARα, 83 are for PPARβ/δ, and 104 are for PPARγ. Detailed information including tissue types, species, and reference PubMed IDs was also provided. In addition, we developed a machine learning method to predict novel PPAR target genes by integratingin silicoPPAR-responsive element (PPRE) analysis with high throughput gene expression data. Fivefold cross validation showed that the performance of this prediction method was significantly improved compared to thein silicoPPRE analysis method. The prediction tool is also implemented in the PPARgene database.

scholarly journals Transcriptional Inhibitors Identified in a 160,000-Compound Small-Molecule DUX4 Viability Screen

2016 ◽  
Vol 21 (7) ◽  
pp. 680-688 ◽  
Author(s):  
Si Ho Choi ◽  
Darko Bosnakovski ◽  
Jessica M. Strasser ◽  
Erik A. Toso ◽  
Michael A. Walters ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Muscular Dystrophy ◽  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Oxidative Stress Pathway ◽  
Nonspecific Effects ◽  
Stress Pathway ◽  
Mouse Myoblast

Facioscapulohumeral muscular dystrophy is a genetically dominant, currently untreatable muscular dystrophy. It is caused by mutations that enable expression of the normally silent DUX4 gene, which encodes a pathogenic transcription factor. A screen based on Tet-on DUX4-induced mouse myoblast death previously uncovered compounds from a 44,000-compound library that protect against DUX4 toxicity. Many of those compounds acted downstream of DUX4 in an oxidative stress pathway. Here, we extend this screen to an additional 160,000 compounds and, using greater stringency, identify a new set of DUX4-protective compounds. From 640 hits, we performed secondary screens, repurchased 46 of the most desirable, confirmed activity, and tested each for activity against other cell death–inducing insults. The majority of these compounds also protected against oxidative stress. Of the 100 repurchased compounds identified through both screens, only SHC40, 75, and 98 inhibited DUX4 target genes, but they also inhibited dox-mediated DUX4 expression. Using a target gene readout on the 640-compound hit set, we discovered three overlooked compounds, SHC351, 540, and 572, that inhibit DUX4 target gene upregulation without nonspecific effects on the Tet-on system. These novel inhibitors of DUX4 transcriptional activity may thus act on pathways or cofactors needed by DUX4 for transcriptional activation in these cells.

scholarly journals Sp5 and Sp8 recruit β-catenin and Tcf1-Lef1 to select enhancers to activate Wnt target gene transcription

2016 ◽  
Vol 113 (13) ◽  
pp. 3545-3550 ◽  
Author(s):  
Mark W. Kennedy ◽  
Ravindra B. Chalamalasetty ◽  
Sara Thomas ◽  
Robert J. Garriock ◽  
Parthav Jailwala ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Gene ◽  
Target Genes ◽  
Wnt Signaling Pathway ◽  
Embryonic Stem ◽  
T Cell Factor ◽  
Core Components ◽  
Specificity Protein ◽  
Wnt Signal ◽  
Target Gene Transcription

The ancient, highly conserved, Wnt signaling pathway regulates cell fate in all metazoans. We have previously shown that combined null mutations of the specificity protein (Sp) 1/Klf-like zinc-finger transcription factors Sp5 and Sp8 (i.e., Sp5/8) result in an embryonic phenotype identical to that observed when core components of the Wnt/β-catenin pathway are mutated; however, their role in Wnt signal transduction is unknown. Here, we show in mouse embryos and differentiating embryonic stem cells that Sp5/8 are gene-specific transcriptional coactivators in the Wnt/β-catenin pathway. Sp5/8 bind directly to GC boxes in Wnt target gene enhancers and to adjacent, or distally positioned, chromatin-bound T-cell factor (Tcf) 1/lymphoid enhancer factor (Lef) 1 to facilitate recruitment of β-catenin to target gene enhancers. Because Sp5 is itself directly activated by Wnt signals, we propose that Sp5 is a Wnt/β-catenin pathway-specific transcripton factor that functions in a feed-forward loop to robustly activate select Wnt target genes.

scholarly journals Peroxisome Proliferator-Activated Receptor γ Target Gene Encoding a Novel Angiopoietin-Related Protein Associated with Adipose Differentiation

2000 ◽  
Vol 20 (14) ◽  
pp. 5343-5349 ◽  
Author(s):  
J. Cliff Yoon ◽  
Troy W. Chickering ◽  
Evan D. Rosen ◽  
Barry Dussault ◽  
Yubin Qin ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Time Course ◽  
Target Gene ◽  
Target Genes ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Isolation And Characterization ◽  
Adipose Differentiation ◽  
Novel Target

ABSTRACT The nuclear receptor peroxisome proliferator-activated receptor γ regulates adipose differentiation and systemic insulin signaling via ligand-dependent transcriptional activation of target genes. However, the identities of the biologically relevant target genes are largely unknown. Here we describe the isolation and characterization of a novel target gene induced by PPARγ ligands, termed PGAR (for PPARγ angiopoietin related), which encodes a novel member of the angiopoietin family of secreted proteins. The transcriptional induction of PGAR follows a rapid time course typical of immediate-early genes and occurs in the absence of protein synthesis. The expression of PGAR is predominantly localized to adipose tissues and placenta and is consistently elevated in genetic models of obesity. Hormone-dependent adipocyte differentiation coincides with a dramatic early induction of the PGAR transcript. Alterations in nutrition and leptin administration are found to modulate the PGAR expression in vivo. Taken together, these data suggest a possible role for PGAR in the regulation of systemic lipid metabolism or glucose homeostasis.

scholarly journals A Functional Interaction between RIP140 and PGC-1α Regulates the Expression of the Lipid Droplet Protein CIDEA

2008 ◽  
Vol 28 (22) ◽  
pp. 6785-6795 ◽  
Author(s):  
Magnus Hallberg ◽  
Daniel L. Morganstein ◽  
Evangelos Kiskinis ◽  
Kunal Shah ◽  
Anastasia Kralli ◽  
...  
Keyword(s):  
Lipid Droplets ◽  
Energy Homeostasis ◽  
Target Gene ◽  
Target Genes ◽  
Cell Function ◽  
Functional Interaction ◽  
Brown Adipocytes ◽  
Target Gene Transcription ◽  
Lipid Droplet Protein ◽  
Estrogen Related Receptor

ABSTRACT Nuclear receptors activate or repress target genes depending on the recruitment of coactivators or corepressors. The corepressor RIP140 and the PPAR coactivator 1α (PGC-1α) both play key roles in the regulated transcription of genes involved in energy homeostasis. We investigated the roles of RIP140 and PGC-1α in controlling the expression of CIDEA, an important regulatory factor in adipose cell function and obesity. Ectopically expressed CIDEA surrounded lipid droplets in brown adipocytes and induced the formation of lipid droplets in nonadipogenic cell lines. The expression and promoter activity of CIDEA was repressed by RIP140 and induced by PGC-1α, mediated through the binding of estrogen-related receptor α and NRF-1 to their cognate binding sites. Importantly, we demonstrate that RIP140 interacts directly with PGC-1α and suppresses its activity. The direct antagonism of PGC-1α by RIP140 provides a mechanism for regulating target gene transcription via nuclear receptor-dependent and -independent pathways.

scholarly journals Liver X Receptor Ligands Suppress Ubiquitination and Degradation of LXRα by Displacing BARD1/BRCA1

2009 ◽  
Vol 23 (4) ◽  
pp. 466-474 ◽  
Author(s):  
Kang Ho Kim ◽  
Jeong Min Yoon ◽  
A Hyun Choi ◽  
Woo Sik Kim ◽  
Gha Young Lee ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Cancer Susceptibility ◽  
Liver X Receptor ◽  
Lipid Homeostasis ◽  
Gene Promoters ◽  
Receptor Ligands ◽  
Ubiquitin E3 Ligase ◽  
Ligand Free

Abstract Liver X receptor (LXR) is a ligand-activated transcription factor that plays important roles in cholesterol and lipid homeostasis. However, ligand-induced posttranslational modification of LXR is largely unknown. Here, we show that ligand-free LXRα is rapidly degraded by ubiquitination. Without ligand, LXRα interacts with an ubiquitin E3-ligase protein complex containing breast and ovarian cancer susceptibility 1 (BRCA1)-associated RING domain 1 (BARD1). Interestingly, LXR ligand represses ubiquitination and degradation of LXRα, and the interaction between LXRα and BARD1 is inhibited by LXR ligand. Consistently, T0901317, a synthetic LXR ligand, increased the level of LXRα protein in liver. Moreover, overexpression of BARD1/BRCA1 promoted the ubiquitination of LXRα and reduced the recruitment of LXRα to the target gene promoters, whereas BARD1 knockdown reversed such effects. Taken together, these data suggest that LXR ligand prevents LXRα from ubiquitination and degradation by detaching BARD1/BRCA1, which might be critical for the early step of transcriptional activation of ligand-stimulated LXRα through a stable binding of LXRα to the promoters of target genes.

Controlling Hematopoiesis through Sumoylation-Dependent Regulation of a GATA Factor.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1467-1467
Author(s):  
Hsiang-Ying Lee ◽  
Kirby D. Johnson ◽  
Tohru Fujiwara ◽  
Meghan E. Boyer ◽  
Shin-Il Kim ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Nuclear Periphery ◽  
Transcriptional Networks ◽  
Gata Factor ◽  
Megakaryoblastic Leukemia ◽  
N Terminus

Abstract Abstract 1467 Poster Board I-490 GATA factors function via distinct modes to establish transcriptional networks that control fundamental developmental processes including hematopoiesis. Whereas the master regulator of hematopoiesis GATA-1 is subject to multiple posttranslational modifications, how these modifications influence GATA-1 activity at endogenous loci is poorly understood. GATA-1 is sumoylated at K137, which resides in the N-terminus, but how the N-terminus contributes to GATA-1 function remains unclear. Expression of a GATA-1 mutant lacking amino acids 1-83 of the N-terminus is linked to the development of acute megakaryoblastic leukemia [Wechsler et al. (2002) Nat. Genet. 32, 148], and deletion of the N-terminus preferentially deregulates a subset of target genes [Johnson et al. (2006) PNAS. 103, 15939]. We demonstrate that sumoylation at K137 promotes transcriptional activation only at a subset of its target genes – those requiring the cell type-specific coregulator, Friend of GATA-1 (FOG-1). Interestingly, a GATA-1 mutation that disrupts FOG-1 binding (V205G) and K137 mutations yielded similar phenotypes, although FOG-1 was not required for K137 sumoylation. Both V205 and K137 mutations dysregulated GATA-1 chromatin occupancy at select sites, FOG-1-dependent target gene expression, and were rescued by tethering SUMO-1. While FOG-1- and SUMO-1-dependent genes migrated away from the nuclear periphery upon erythroid maturation, FOG-1- and SUMO-1-independent genes localized at the periphery independent of maturation. These results illustrate how sumoylation of a critical developmental regulator selectively controls its function at specific loci, and members of a target gene ensemble with distinct coregulator and posttranslational modification requirements reside in different subnuclear compartments. Disclosures: No relevant conflicts of interest to declare.

scholarly journals MAML1-Dependent Notch-Responsive Genes Exhibit Differing Cofactor Requirements for Transcriptional Activation

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Julia M. Rogers ◽  
Bingqian Guo ◽  
Emily D. Egan ◽  
Jon C. Aster ◽  
Karen Adelman ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Target Gene ◽  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Transcriptional Responses ◽  
Jurkat T Cell ◽  
Recruitment Activities ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Molecular Complexity ◽  
Transcriptional Induction

ABSTRACT Mastermind proteins are required for transcription of Notch target genes, yet the molecular basis for mastermind function remains incompletely understood. Previous work has shown that Notch can induce transcriptional responses by binding to promoters but more often by binding to enhancers, with HES4 and DTX1 as representative mammalian examples of promoter and enhancer responsiveness, respectively. Here, we show that mastermind dependence of the Notch response at these loci is differentially encoded in Jurkat T-cell acute lymphoblastic leukemia (T-ALL) cells. Knockout of Mastermind-like 1 (MAML1) eliminates Notch-responsive activation of both these genes, and reduced target gene expression is accompanied by a decrease in H3K27 acetylation, consistent with the importance of MAML1 for p300 activity. Add-back of MAML1 variants in knockout cells identifies residues 151 to 350 of MAML1 as essential for expression of either Notch-responsive gene. Fusion of the Notch-binding region of MAML1 to the histone acetyltransferase (HAT) domain of p300 rescues expression of HES4 but not DTX1, suggesting that an additional activity of MAML1 is needed for gene induction at a distance. Together, these studies establish the functional importance of the MAML1 region from residues 151 to 350 for Notch-dependent transcriptional induction and reveal differential requirements for MAML1-dependent recruitment activities at different Notch-responsive loci, highlighting the molecular complexity of Notch-stimulated transcription.

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