TSHZ2 is an EGF-regulated tumor suppressor that binds to the cytokinesis regulator PRC1 and inhibits metastasis

Unlike early transcriptional responses to mitogens, later events are less well-characterized. Here, we identified delayed down-regulated genes (DDGs) in mammary cells after prolonged treatment with epidermal growth factor (EGF). The expression of these DDGs was low in mammary tumors and correlated with prognosis. The proteins encoded by several DDGs directly bind to and inactivate oncoproteins and might therefore act as tumor suppressors. The transcription factor teashirt zinc finger homeobox 2 (TSHZ2) is encoded by a DDG, and we found that overexpression of TSHZ2 inhibited tumor growth and metastasis and accelerated mammary gland development in mice. Although the gene TSHZ2 localizes to a locus (20q13.2) that is frequently amplified in breast cancer, we found that hypermethylation of its promoter correlated with down-regulation of TSHZ2 expression in patients. Yeast two-hybrid screens and protein-fragment complementation assays in mammalian cells indicated that TSHZ2 nucleated a multiprotein complex containing PRC1/Ase1, cyclin B1, and additional proteins that regulate cytokinesis. TSHZ2 increased the inhibitory phosphorylation of PRC1, a key driver of mitosis, mediated by cyclin-dependent kinases. Furthermore, similar to the tumor suppressive transcription factor p53, TSHZ2 inhibited transcription from the PRC1 promoter. By recognizing DDGs as a distinct group in the transcriptional response to EGF, our findings uncover a group of tumor suppressors and reveal a role for TSHZ2 in cell cycle regulation.

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Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells

eLife ◽

10.7554/elife.07687 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 16

Author(s):

Yusuke Miyazaki ◽

Ling-chun Chen ◽

Bernard W Chu ◽

Tomek Swigut ◽

Thomas J Wandless

Keyword(s):

Mammalian Cells ◽

Cellular Response ◽

Protein Quality ◽

Transcriptional Response ◽

Central Component ◽

Unfolded Proteins ◽

Transcriptional Responses ◽

Control Networks ◽

Unfolded Protein ◽

Sudden Appearance

Eukaryotic cells possess a variety of signaling pathways that prevent accumulation of unfolded and misfolded proteins. Chief among these is the heat shock response (HSR), which is assumed to respond to unfolded proteins in the cytosol and nucleus alike. In this study, we probe this axiom further using engineered proteins called ‘destabilizing domains’, whose folding state we control with a small molecule. The sudden appearance of unfolded protein in mammalian cells elicits a robust transcriptional response, which is distinct from the HSR and other known pathways that respond to unfolded proteins. The cellular response to unfolded protein is strikingly different in the nucleus and the cytosol, although unfolded protein in either compartment engages the p53 network. This response provides cross-protection during subsequent proteotoxic stress, suggesting that it is a central component of protein quality control networks, and like the HSR, is likely to influence the initiation and progression of human pathologies.

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A Role for Iron-Sulfur Clusters in the Regulation of Transcription Factor Yap5-dependent High Iron Transcriptional Responses in Yeast

Journal of Biological Chemistry ◽

10.1074/jbc.m112.395533 ◽

2012 ◽

Vol 287 (42) ◽

pp. 35709-35721 ◽

Cited By ~ 37

Author(s):

Liangtao Li ◽

Ren Miao ◽

Sophie Bertram ◽

Xuan Jia ◽

Diane M. Ward ◽

...

Keyword(s):

Transcription Factor ◽

Target Genes ◽

Transcriptional Response ◽

Regulation Of Transcription ◽

Transcriptional Responses ◽

Iron Sulfur Cluster ◽

Iron Sulfur Clusters ◽

Sulfur Cluster ◽

High Iron ◽

Iron Sulfur

Yeast respond to increased cytosolic iron by activating the transcription factor Yap5 increasing transcription of CCC1, which encodes a vacuolar iron importer. Using a genetic screen to identify genes involved in Yap5 iron sensing, we discovered that a mutation in SSQ1, which encodes a mitochondrial chaperone involved in iron-sulfur cluster synthesis, prevented expression of Yap5 target genes. We demonstrated that mutation or reduced expression of other genes involved in mitochondrial iron-sulfur cluster synthesis (YFH1, ISU1) prevented induction of the Yap5 response. We took advantage of the iron-dependent catalytic activity of Pseudaminobacter salicylatoxidans gentisate 1,2-dioxygenase expressed in yeast to measure changes in cytosolic iron. We determined that reductions in iron-sulfur cluster synthesis did not affect the activity of cytosolic gentisate 1,2-dioxygenase. We show that loss of activity of the cytosolic iron-sulfur cluster assembly complex proteins or deletion of cytosolic glutaredoxins did not reduce expression of Yap5 target genes. These results suggest that the high iron transcriptional response, as well as the low iron transcriptional response, senses iron-sulfur clusters.

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The Role of Heat Shock Transcription Factor 1 in the Genome-wide Regulation of the Mammalian Heat Shock Response

Molecular Biology of the Cell ◽

10.1091/mbc.e03-10-0738 ◽

2004 ◽

Vol 15 (3) ◽

pp. 1254-1261 ◽

Cited By ~ 222

Author(s):

Nathan D. Trinklein ◽

John I. Murray ◽

Sara J. Hartman ◽

David Botstein ◽

Richard M. Myers

Keyword(s):

Transcription Factor ◽

Heat Shock ◽

Heat Shock Response ◽

Mammalian Cells ◽

Transcriptional Response ◽

Heat Shock Transcription Factor ◽

Genome Wide ◽

Shock Response ◽

Inducible Genes ◽

Transcription Factor 1

Previous work has implicated heat shock transcription factor 1 (HSF1) as the primary transcription factor responsible for the transcriptional response to heat stress in mammalian cells. We characterized the heat shock response of mammalian cells by measuring changes in transcript levels and assaying binding of HSF1 to promoter regions for candidate heat shock genes chosen by a combination of genome-wide computational and experimental methods. We found that many heat-inducible genes have HSF1 binding sites (heat shock elements, HSEs) in their promoters that are bound by HSF1. Surprisingly, for 24 heat-inducible genes, we detected no HSEs and no HSF1 binding. Furthermore, of 182 promoters with likely HSE sequences, we detected HSF1 binding at only 94 of these promoters. Also unexpectedly, we found 48 genes with HSEs in their promoters that are bound by HSF1 but that nevertheless did not show induction after heat shock in the cell types we examined. We also studied the transcriptional response to heat shock in fibroblasts from mice lacking the HSF1 gene. We found 36 genes in these cells that are induced by heat as well as they are in wild-type cells. These results provide evidence that HSF1 does not regulate the induction of every transcript that accumulates after heat shock, and our results suggest that an independent posttranscriptional mechanism regulates the accumulation of a significant number of transcripts.

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Permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver

10.1101/2021.03.10.434889 ◽

2021 ◽

Author(s):

Anjana Ramdas Nair ◽

Priyanka Lakhiani ◽

Chi Zhang ◽

Filippo Macchi ◽

Kirsten C. Sadler

Keyword(s):

Transcription Factor ◽

Target Genes ◽

Expression Patterns ◽

Transcriptional Response ◽

Differentially Expressed ◽

Small Subset ◽

Gene Promoters ◽

Transcriptional Responses ◽

Functional Studies ◽

Activating Transcription Factor

ABSTRACTProteostatic stress initiates a transcriptional response that is unique to the stress condition, yet the regulatory mechanisms underlying the distinct gene expression patterns observed in stressed cells remains unknown. Using a functional genomic approach, we investigated how activating transcription factor 6 (ATF6), a key transcription factor in the unfolded protein response (UPR), regulates target genes. We first designed a computational strategy to define Atf6 target genes based on the evolutionary conservation of predicted ATF6 binding in gene promoters, identifying 652 conserved putative Atf6 target (CPAT) genes. CPATs were overrepresented for genes functioning in the UPR, however, the majority functioned in cellular processes unrelated to proteostasis, including small molecule metabolism and development. Functional studies of stress-independent and toxicant based Atf6 activation in zebrafish livers showed that the pattern of CPAT expression in response to Atf6 overexpression, alcohol and arsenic was unique. Only 34 CPATs were differentially expressed in all conditions, indicating that Atf6 is sufficient to regulate a small subset of CPATs. Blocking Atf6 using Ceapins in zebrafish demonstrated that Atf6 is necessary for activation of these genes in response to arsenic. We investigated CPAT during physiologically mediated hepatocyte stress using liver regeneration in mice as a model. Over half of all CPATs were differentially expressed during this process. This was attributed to the permissive chromatin environment in quiescent livers on the promoters of these genes, characterized by the absence of H3K27me3 and enrichment of H3K4me3. Taken together, these data uncover a complex transcriptional response to Atf6 activation and implicate a permissive epigenome as a mechanism by which distinct transcriptional responses are regulated by Atf6.

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Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

10.1101/117689 ◽

2017 ◽

Cited By ~ 1

Author(s):

Noah Dukler ◽

Gregory T. Booth ◽

Yi-Fei Huang ◽

Nathaniel Tippens ◽

Charles G. Danko ◽

...

Keyword(s):

Time Course ◽

Transcriptional Response ◽

Distinct Group ◽

K562 Cells ◽

Careful Analysis ◽

Transcriptional Responses ◽

Time Course Data ◽

Nascent Rna ◽

Polymerase Pausing ◽

Key Aspects

AbstractMost studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours, and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory and obesity-controlling effects. Our analysis of PRO-seq data for K562 cells reveals dramatic transcriptional effects soon after celastrol treatment at a broad collection of both coding and noncoding transcription units. This transcriptional response occurred in two major waves, one within 10 minutes, and a second 40-60 minutes after treatment. Transcriptional activity was generally repressed by celastrol, but one distinct group of genes, enriched for roles in the heat shock response, displayed strong activation. Using a regression approach, we identified key transcription factors that appear to drive these transcriptional responses, including members of the E2F and RFX families. We also found sequence-based evidence that particular TFs drive the activation of enhancers. We observed increased polymerase pausing at both genes and enhancers, suggesting that pause release may be widely inhibited during the celastrol response. Our study demonstrates that a careful analysis of PRO-seq time course data can disentangle key aspects of a complex transcriptional response, and it provides new insights into the activity of a powerful pharmacological agent.

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Fungal Zn(II)2Cys6 Transcription Factor ADS-1 Regulates Drug Efflux and Ergosterol Metabolism Under Antifungal Azole Stress

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01316-20 ◽

2020 ◽

Author(s):

Yajing Yin ◽

Hanxing Zhang ◽

Yu Zhang ◽

Chengcheng Hu ◽

Xianyun Sun ◽

...

Keyword(s):

Transcription Factor ◽

Efflux Pump ◽

Transcriptional Response ◽

Fungal Species ◽

Antifungal Drugs ◽

Regulatory Function ◽

Ergosterol Biosynthesis ◽

Agricultural Practice ◽

Transcriptional Responses ◽

Basal Resistance

Antifungal azoles are the most widely used antifungal drugs in clinical and agricultural practice. Fungi can make adaptive responses to azole stress by modifying transcript levels of many genes and the responsive mechanisms to azoles are the basis for fungi to develop azole resistance. In this study, we identified a new Zn(II)2Cys6 transcription factor ADS-1 with a positive regulatory function in transcriptional responses to azole stress in the model filamentous fungal species Neurospora crassa. Under ketoconazole (KTC) stress, the transcript level of ads-1 was significantly increased in N. crassa. Deletion of ads-1 increased the susceptibility to different azoles while its overexpression increased resistance to these azoles. The gene cdr4, which encodes the key azole efflux pump, was positively regulated by ADS-1. Deletion of ads-1 reduced the transcriptional response by cdr4 to KTC stress and increased the cellular KTC accumulation under KTC stress while its overexpression had the opposite effect. ADS-1 also positively regulated transcriptional response by erg11, which encodes the azole target lanosterol 14α-demethylase for ergosterol biosynthesis, to KTC stress. After KTC treatment, the ads-1 deletion mutant had less ergosterol but accumulated more lanosterol than wild type, while ads-1 overexpression had the opposite effects. The homologs of ADS-1 widely present in filamentous fungal species of Ascomycota but not in yeasts. Deletion of the gene encoding ADS-1 homolog in Aspergillus flavus also increased the susceptibility to KTC and itraconazole (ITZ). Besides, deletion of Afads-1 significantly reduced the transcriptional response by genes encoding homologs of CDR4 and ERG11 in A. flavus to KTC stress and accumulated more KTC but less ergosterol. Together, the function and regulatory mechanism of ADS-1 homologs among different fungal species in azole responses and the basal resistance of azoles are highly conserved.

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Transcriptional Response of Saccharomyces cerevisiae to the Plasma Membrane-Perturbing Compound Chitosan

Eukaryotic Cell ◽

10.1128/ec.4.4.703-715.2005 ◽

2005 ◽

Vol 4 (4) ◽

pp. 703-715 ◽

Cited By ~ 102

Author(s):

Anna Zakrzewska ◽

Andre Boorsma ◽

Stanley Brul ◽

Klaas J. Hellingwerf ◽

Frans M. Klis

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Wall ◽

Transcription Factor ◽

Plasma Membrane ◽

Transcriptional Response ◽

Wall Stress ◽

Yeast Cells ◽

Transcriptional Responses ◽

Cell Wall Stress ◽

Spoilage Yeast

ABSTRACT Chitosan is a plasma membrane-perturbing compound consisting of linear chains of β-1,4-linked glucosamine residues, which at acidic pHs become positively charged. It is extensively used as an antimicrobial compound, yet its mode of action is still unresolved. Chitosan strongly affected the growth of the yeast Saccharomyces cerevisiae, the food spoilage yeast Zygosaccharomyces bailii, and two human-pathogenic yeasts, Candida albicans and Candida glabrata. Microarray analysis of yeast cells treated with sublethal concentrations of chitosan revealed induction of the environmental stress response and three more major transcriptional responses. The first was a rapid and stable Cin5p-mediated response. Cin5p/Yap4p is a transcription factor involved in various stress responses. Deletion of CIN5 led to increased chitosan sensitivity. The second was a Crz1p-mediated response, which is delayed compared to the Cin5p response. Crz1p is a transcription factor of the calcineurin pathway. Cells deleted for CRZ1 or treated with the calcineurin inhibitor FK506 became hypersensitive to chitosan, supporting the notion that the Crz1p-controlled response offers protection against chitosan. The third was a strong Rlm1p-mediated response which ran parallel in time with the Crz1p-regulated response. Rlm1p is a transcription factor of the cell wall integrity pathway, which is activated by cell wall stress. Importantly, chitosan-treated cells became more resistant to β-1,3-glucanase, which is a well-known response to cell wall stress. We propose that the transcriptional response to chitosan may be representative of other plasma membrane-perturbing compounds.

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Efg1 and Cas5 Orchestrate Cell Wall Damage Response to Caspofungin in Candida albicans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01584-20 ◽

2020 ◽

Author(s):

Kang Xiong ◽

Chang Su ◽

Qiangqiang Sun ◽

Yang Lu

Keyword(s):

Cell Wall ◽

Transcription Factor ◽

Candida Albicans ◽

Transcriptional Response ◽

Wall Stress ◽

Growth Defect ◽

Transcriptional Responses ◽

Cell Wall Stress ◽

Cell Wall Damage

Echinocandins are recommended as the first-line drugs for the treatment of systemic candidiasis. Cas5 is a key transcription factor involved in the response to cell wall damage induced by echinocandins. Here, through a genetic screen, we report the identification of a second transcription factor Efg1 that is also crucial for proper transcriptional responses to echinocandins. Like CAS5, deletion of EFG1 confers hypersensitivity to caspofungin. Efg1 is required for the induction of CAS5 in response to caspofungin. However, ectopically expressed CAS5 cannot rescue the growth defect of efg1 mutant in caspofungin-containing medium. Deleting EFG1 in the cas5 mutant exacerbates the cell wall stress upon caspofungin addition and renders caspofungin-resistant Candida albicans responsive to treatment. Genome-wide transcription profiling of efg1/efg1 and cas5/cas5 using a RNA-Seq indicates that Efg1 and Cas5 co-regulate numbers of caspofungin-responsive genes expression, but they also independently control some genes induction. We further show that Efg1 interacts with Cas5 by yeast two-hybrid and in vivo immunoprecipitation in the presence or absence of caspofungin. Importantly, Efg1 and Cas5 bind to some caspofungin-responsive genes promoter to coordinately activate their expression. Thus, we demonstrate that Efg1, together with Cas5, controls the transcriptional response to cell wall stress induced by caspofungin.

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Transcription factor p53 can regulate proliferation, apoptosis and secretory activity of luteinizing porcine ovarian granulosa cell cultured with and without ghrelin and FSH

Reproduction ◽

10.1530/rep-08-0229 ◽

2008 ◽

Vol 136 (5) ◽

pp. 611-618 ◽

Cited By ~ 31

Author(s):

A V Sirotkin ◽

A Benčo ◽

A Tandlmajerova ◽

D Vašíček ◽

J Kotwica ◽

...

Keyword(s):

Transcription Factor ◽

Granulosa Cells ◽

P53 Gene ◽

Secretory Activity ◽

Cyclin B1 ◽

Over Expression ◽

Gene Construct ◽

Ovarian Cells ◽

Transcription Factor P53

The aim of our in vitro experiments was to examine the role of transcription factor p53 in controlling the basic functions of ovarian cells and their response to hormonal treatments. Porcine ovarian granulosa cells, transfected and non-transfected with a gene construct encoding p53, were cultured with ghrelin and FSH (all at concentrations of 0, 1, 10, or 100 ng/ml). Accumulation of p53, of apoptosis-related (MAP3K5) and proliferation-related (cyclin B1) substances was evaluated by immunocytochemistry. The secretion of progesterone (P4), oxytocin (OT), prostaglandin F (PGF), and E (PGE) was measured by RIA. Transfection with the p53 gene construct promoted accumulation of this transcription factor within cells. It also stimulated the expression of a marker of apoptosis (MAP3K5). Over-expression of p53 resulted in reduced accumulation of a marker of proliferation (cyclin B1), P4, and PGF secretion and increased OT and PGE secretion. Ghrelin, when added alone, did not affect p53 or P4, but reduced MAP3K5 and increased PGF and PGE secretion. Over-expression of p53 reversed the effect of ghrelin on OT, caused it to be inhibitory to P4 secretion, but did not modify its action on MAP3K5, PGF, or PGE. FSH promoted the accumulation of p53, MAP3K5, and cyclin B1; these effects were unaffected by p53 transfection. These multiple effects of the p53 gene construct on luteinizing granulosa cells, cultured with and without hormones 1) demonstrate the effects of ghrelin and FSH on porcine ovarian cell apoptosis and secretory activity, 2) confirm the involvement of p53 in promoting apoptosis and inhibiting P4 secretion in these cells, 3) provide the first evidence that p53 suppress proliferation of ovarian cells, 4) provide the first evidence that p53 is involved in the control of ovarian peptide hormone (OT) and prostaglandin (PGF and PGE) secretion, and 5) suggest that p53 can modulate, but probably not mediate, the effects of ghrelin and FSH on the ovary.

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EspM Is a Conserved Transcription Factor That Regulates Gene Expression in Response to the ESX-1 System

mBio ◽

10.1128/mbio.02807-19 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 3

Author(s):

Kevin G. Sanchez ◽

Micah J. Ferrell ◽

Alexandra E. Chirakos ◽

Kathleen R. Nicholson ◽

Robert B. Abramovitch ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Protein Transport ◽

Transcriptional Response ◽

Secretion System ◽

Pathogenic Species ◽

Macrophage Infection ◽

Content Type ◽

Link Type ◽

Phagosomal Membrane

ABSTRACT Pathogenic mycobacteria encounter multiple environments during macrophage infection. Temporally, the bacteria are engulfed into the phagosome, lyse the phagosomal membrane, and interact with the cytosol before spreading to another cell. Virulence factors secreted by the mycobacterial ESX-1 (ESAT-6-system-1) secretion system mediate the essential transition from the phagosome to the cytosol. It was recently discovered that the ESX-1 system also regulates mycobacterial gene expression in Mycobacterium marinum (R. E. Bosserman, T. T. Nguyen, K. G. Sanchez, A. E. Chirakos, et al., Proc Natl Acad Sci U S A 114:E10772–E10781, 2017, https://doi.org/10.1073/pnas.1710167114), a nontuberculous mycobacterial pathogen, and in the human-pathogenic species M. tuberculosis (A. M. Abdallah, E. M. Weerdenburg, Q. Guan, R. Ummels, et al., PLoS One 14:e0211003, 2019, https://doi.org/10.1371/journal.pone.0211003). It is not known how the ESX-1 system regulates gene expression. Here, we identify the first transcription factor required for the ESX-1-dependent transcriptional response in pathogenic mycobacteria. We demonstrate that the gene divergently transcribed from the whiB6 gene and adjacent to the ESX-1 locus in mycobacterial pathogens encodes a conserved transcription factor (MMAR_5438, Rv3863, now espM). We prove that EspM from both M. marinum and M. tuberculosis directly and specifically binds the whiB6-espM intergenic region. We show that EspM is required for ESX-1-dependent repression of whiB6 expression and for the regulation of ESX-1-associated gene expression. Finally, we demonstrate that EspM functions to fine-tune ESX-1 activity in M. marinum. Taking the data together, this report extends the esx-1 locus, defines a conserved regulator of the ESX-1 virulence pathway, and begins to elucidate how the ESX-1 system regulates gene expression. IMPORTANCE Mycobacterial pathogens use the ESX-1 system to transport protein substrates that mediate essential interactions with the host during infection. We previously demonstrated that in addition to transporting proteins, the ESX-1 secretion system regulates gene expression. Here, we identify a conserved transcription factor that regulates gene expression in response to the ESX-1 system. We demonstrate that this transcription factor is functionally conserved in M. marinum, a pathogen of ectothermic animals; M. tuberculosis, the human-pathogenic species that causes tuberculosis; and M. smegmatis, a nonpathogenic mycobacterial species. These findings provide the first mechanistic insight into how the ESX-1 system elicits a transcriptional response, a function of this protein transport system that was previously unknown.

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