An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output

SummaryWhile precise tuning of gene expression levels is critical for most developmental pathways, the mechanisms by which the transcriptional output of dosage-sensitive molecules is established or modulated by the environment remain poorly understood. Here, we provide a mechanistic framework for how the conserved transcription factor BLMP-1/Blimp1 operates as a pioneer factor to decompact chromatin near its target loci hours before transcriptional activation and by doing so, regulates both the duration and amplitude of subsequent target gene transcription. This priming mechanism is genetically separable from the mechanisms that establish the timing of transcriptional induction and functions to canalize aspects of cell-fate specification, animal size regulation, and molting. A key feature of the BLMP-1-dependent transcriptional priming mechanism is that chromatin decompaction is initially established during embryogenesis and maintained throughout larval development by nutrient sensing. This anticipatory mechanism integrates transcriptional output with environmental conditions and is essential for resuming normal temporal patterning after animals exit nutrient-mediated developmental arrests.

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Frazzled/Dcc acts independently of Netrin to promote germline survival during Drosophila oogenesis

Development ◽

10.1242/dev.199762 ◽

2021 ◽

Vol 148 (24) ◽

Author(s):

Samantha A. Russell ◽

Kaitlin M. Laws ◽

Greg J. Bashaw

Keyword(s):

Cell Death ◽

Axon Guidance ◽

Transcriptional Activation ◽

Nutrient Sensing ◽

Activation Domain ◽

Transcriptional Activation Domain ◽

Egg Chambers ◽

Death Effector ◽

Female Germline

ABSTRACT The Netrin receptor Frazzled/Dcc (Fra in Drosophila) functions in diverse tissue contexts to regulate cell migration, axon guidance and cell survival. Fra signals in response to Netrin to regulate the cytoskeleton and also acts independently of Netrin to directly regulate transcription during axon guidance in Drosophila. In other contexts, Dcc acts as a tumor suppressor by directly promoting apoptosis. In this study, we report that Fra is required in the Drosophila female germline for the progression of egg chambers through mid-oogenesis. Loss of Fra in the germline, but not the somatic cells of the ovary, results in the degeneration of egg chambers. Although a failure in nutrient sensing and disruptions in egg chamber polarity can result in degeneration at mid-oogenesis, these factors do not appear to be affected in fra germline mutants. However, similar to the degeneration that occurs in those contexts, the cell death effector Dcp-1 is activated in fra germline mutants. The function of Fra in the female germline is independent of Netrin and requires the transcriptional activation domain of Fra. In contrast to the role of Dcc in promoting cell death, our observations reveal a role for Fra in regulating germline survival by inhibiting apoptosis.

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H3 K79 dimethylation marks developmental activation of the β-globin gene but is reduced upon LCR-mediated high-level transcription

Blood ◽

10.1182/blood-2007-12-128983 ◽

2008 ◽

Vol 112 (2) ◽

pp. 406-414 ◽

Cited By ~ 11

Author(s):

Tomoyuki Sawado ◽

Jessica Halow ◽

Hogune Im ◽

Tobias Ragoczy ◽

Emery H. Bresnick ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Activation ◽

Globin Gene ◽

Erythroid Differentiation ◽

Genome Wide ◽

Activation Of Transcription ◽

High Level ◽

The Relationship ◽

Mutant Genes ◽

Gene Expression Levels

Abstract Genome-wide analyses of the relationship between H3 K79 dimethylation and transcription have revealed contradictory results. To clarify this relationship at a single locus, we analyzed expression and H3 K79 modification levels of wild-type (WT) and transcriptionally impaired β-globin mutant genes during erythroid differentiation. Analysis of fractionated erythroid cells derived from WT/Δ locus control region (LCR) heterozygous mice reveals no significant H3 K79 dimethylation of the β-globin gene on either allele prior to activation of transcription. Upon transcriptional activation, H3 K79 di-methylation is observed along both WT and ΔLCR alleles, and both alleles are located in proximity to H3 K79 dimethylation nuclear foci. However, H3 K79 di-methylation is significantly increased along the ΔLCR allele compared with the WT allele. In addition, analysis of a partial LCR deletion mutant reveals that H3 K79 dimethylation is inversely correlated with β-globin gene expression levels. Thus, while our results support a link between H3 K79 dimethylation and gene expression, high levels of this mark are not essential for high level β-globin gene transcription. We propose that H3 K79 dimethylation is destabilized on a highly transcribed template.

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Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomyces cerevisiae Ste12p.

Molecular and Cellular Biology ◽

10.1128/mcb.17.11.6410 ◽

1997 ◽

Vol 17 (11) ◽

pp. 6410-6418 ◽

Cited By ~ 44

Author(s):

H Pi ◽

C T Chien ◽

S Fields

Keyword(s):

Saccharomyces Cerevisiae ◽

Map Kinase ◽

Transcriptional Activation ◽

Transcriptional Activity ◽

Activation Domain ◽

Yeast Saccharomyces Cerevisiae ◽

Activation Domains ◽

Hybrid Proteins ◽

High Level ◽

Transcriptional Induction

In the yeast Saccharomyces cerevisiae, Ste12p induces transcription of pheromone-responsive genes by binding to a DNA sequence designated the pheromone response element. We generated a series of hybrid proteins of Ste12p with the DNA-binding and activation domains of the transcriptional activator Gal4p to define a pheromone induction domain of Ste12p sufficient to mediate pheromone-induced transcription by these hybrid proteins. A minimal pheromone induction domain, delineated as residues 301 to 335 of Ste12p, is dependent on the pheromone mitogen-activated protein (MAP) kinase pathway for induction activity. Mutation of the three serine and threonine residues within the minimal pheromone induction domain did not affect transcriptional induction, indicating that the activity of this domain is not directly regulated by MAP kinase phosphorylation. By contrast, mutation of the two tyrosines or their preceding acidic residues led to a high level of transcriptional activity in the absence of pheromone and consequently to the loss of pheromone induction. This constitutively high activity was not affected by mutations in the MAP kinase cascade, suggesting that the function of the pheromone induction domain is normally repressed in the absence of pheromone. By two-hybrid analysis, this minimal domain interacts with two negative regulators, Dig1p and Dig2p (also designated Rst1p and Rst2p), and the interaction is abolished by mutation of the tyrosines. The pheromone induction domain itself has weak and inducible transcriptional activity, and its ability to potentiate transcription depends on the activity of an adjacent activation domain. These results suggest that the pheromone induction domain of Ste12p mediates transcriptional induction via a two-step process: the relief of repression and synergistic transcriptional activation with another activation domain.

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Abstract 356: Krueppel-Like Factor 15 Regulates Wnt/β-Catenin Transcription and Controls Cardiac Progenitor Cell Fate in the Postnatal Heart

Circulation Research ◽

10.1161/res.111.suppl_1.a356 ◽

2012 ◽

Vol 111 (suppl_1) ◽

Author(s):

Claudia Noack ◽

Maria P Zafiriou ◽

Anke Renger ◽

Hans J Schaeffer ◽

Martin W Bergmann ◽

...

Keyword(s):

Cell Fate ◽

Transcriptional Activation ◽

Progenitor Cell ◽

Cellular Localization ◽

Target Genes ◽

Critical Role ◽

Isolated Cells ◽

Cardiac Progenitor Cell

Wnt/β-catenin signaling controls adult heart remodeling partly by regulating cardiac progenitor cell (CPC) differentiation. We now identified and characterized a novel cardiac interaction of the transcription factor Krueppel-like factor 15 (KLF15) with the Wnt/β-catenin signaling on adult CPCs. In vitro mutation, reporter gene assays and co-localization studies revealed that KLF15 requires two distinct domains for nuclear localization and for repression of β-catenin-mediated transcription. KLF15 had no effect on β-catenin stability or cellular localization, but interacted with its co-factor TCF4, which is required for activation of β-catenin target gene expression. Moreover, increased TCF4 ubiquitination was induced by KLF15. In line with this finding we found KLF15 to interact with the Nemo-like kinase, which was shown to phosphorylate and target TCF4 for degradation. In vivo analyses of adult Klf15 functional knock-out (KO) vs. wild-type (WT) mice showed a cardiac β-catenin-mediated transcriptional activation and reduced TCF4 degradation along with cardiac dysfunction assessed by echocardiography (n=10). FACS analysis of the CPC enriched-population of KO vs. WT mice revealed a significant reduction of cardiogenic-committed precursors identified as Sca1+/αMHC+ (0.8±0.2% vs. 1.8±0.1%) and Tbx5+ (3.5±0.3% vs. 5.2±0.5%). In contrast, endothelial Sca1+/CD31+ cells were significantly higher in KO mice (11.3±0.4% vs. 8.6±0.4%; n≥9). In addition, Sca1+ isolated cells of Klf15 KO showed increased RNA expression of endothelial markers von Willebrand Factor, CD105, and Flk1 along with upregulation of β-catenin target genes. CPCs co-cultured on adult fibroblasts resulted in increased endothelial Flk1 cells and reduction of αMHC and Hand1 cardiogenic cells in KO vs. WT CPCs (n=9). Treating these co-cultures with Quercetin, an inhibitor of nuclear β-catenin, resulted in partial rescue of the observed phenotype. This study uncovers a critical role of KLF15 for the maintenance of cardiac tissue homeostasis. Via inhibition of β-catenin transcription, KLF15 controls cardiomyogenic cell fate similar to embryonic cardiogenesis. This knowledge may provide a tool for activation of endogenous CPCs in the postnatal heart.

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The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

Current Biology ◽

10.1016/j.cub.2019.03.019 ◽

2019 ◽

Vol 29 (8) ◽

pp. 1387-1393.e5 ◽

Cited By ~ 24

Author(s):

Shigehiro Yamada ◽

Peter H. Whitney ◽

Shao-Kuei Huang ◽

Elizabeth C. Eck ◽

Hernan G. Garcia ◽

...

Keyword(s):

Pioneer Factor ◽

Transcriptional Output

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Crebl2 regulates cell metabolism in muscle and liver cells

Scientific Reports ◽

10.1038/s41598-019-56407-w ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Marcel Tiebe ◽

Marilena Lutz ◽

Deniz Senyilmaz Tiebe ◽

Aurelio A. Teleman

Keyword(s):

Transcription Factors ◽

Glucose Uptake ◽

Metabolic Response ◽

Cell Metabolism ◽

Cellular Metabolism ◽

Nutrient Sensing ◽

C2c12 Myoblasts ◽

Elevated Glucose ◽

Triglyceride Biosynthesis ◽

Transcriptional Induction

AbstractWe previously identified Drosophila REPTOR and REPTOR-BP as transcription factors downstream of mTORC1 that play an important role in regulating organismal metabolism. We study here the mammalian ortholog of REPTOR-BP, Crebl2. We find that Crebl2 mediates part of the transcriptional induction caused by mTORC1 inhibition. In C2C12 myoblasts, Crebl2 knockdown leads to elevated glucose uptake, elevated glycolysis as observed by lactate secretion, and elevated triglyceride biosynthesis. In Hepa1-6 hepatoma cells, Crebl2 knockdown also leads to elevated triglyceride levels. In sum, this works identifies Crebl2 as a regulator of cellular metabolism that can link nutrient sensing via mTORC1 to the metabolic response of cells.

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TCam-2 Cells Deficient for SOX2 and FOXA2 Are Blocked in Differentiation and Maintain a Seminoma-Like Cell Fate In Vivo

Cancers ◽

10.3390/cancers11050728 ◽

2019 ◽

Vol 11 (5) ◽

pp. 728 ◽

Cited By ~ 1

Author(s):

Daniel Nettersheim ◽

Saskia Vadder ◽

Sina Jostes ◽

Alena Heimsoeth ◽

Hubert Schorle

Keyword(s):

Cell Fate ◽

Primordial Germ Cells ◽

Germ Cell Tumors ◽

Embryonic Stem ◽

Bmp Signaling ◽

Stem Cell Population ◽

Testicular Germ Cell ◽

Key Factor ◽

Pioneer Factor

Testicular germ cell tumors (GCTs) are very common in young men and can be stratified into seminomas and non-seminomas. While seminomas share a similar gene expression and epigenetic profile with primordial germ cells, the stem cell population of the non-seminomas, the embryonal carcinoma (EC), resembles malignant embryonic stem cells. Thus, ECs are able to differentiate into cells of all three germ layers (teratomas) and even extra-embryonic-tissue-like cells (yolk-sac tumor, choriocarcinoma). In the last years, we demonstrated that the cellular microenvironment considerably influences the plasticity of seminomas (TCam-2 cells). Upon a microenvironment-triggered inhibition of the BMP signaling pathway in vivo (murine flank or brain), seminomatous TCam-2 cells reprogram to an EC-like cell fate. We identified SOX2 as a key factor activated upon BMP inhibition mediating the reprogramming process by regulating pluripotency, reprogramming and epigenetic factors. Indeed, CRISPR/Cas9 SOX2-deleted TCam-2 cells were able to maintain a seminoma-cell fate in vivo for about six weeks, but after six weeks in vivo still small sub-populations initiated differentiation. Closer analyses of these differentiated clusters suggested that the pioneer factor FOXA2 might be the driving force behind this induction of differentiation, since many FOXA2 interacting genes and differentiation factors like AFP, EOMES, CDX1, ALB, HAND1, DKK, DLK1, MSX1 and PITX2 were upregulated. In this study, we generated TCam-2 cells double-deficient for SOX2 and FOXA2 using the CRISPR/Cas9 technique and xenografted those cells into the flank of nude mice. Upon loss of SOX2 and FOXA2, TCam-2 maintained a seminoma cell fate for at least twelve weeks, demonstrating that both factors are key players in the reprogramming to an EC-like cell fate. Therefore, our study adds an important piece to the puzzle of GCT development and plasticity, providing interesting insights in what can be expected in a patient, when GCT cells are confronted with different microenvironments.

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Studying the consequences of immediate loss of gene function in the intestine: APC

Biochemical Society Transactions ◽

10.1042/bst0330665 ◽

2005 ◽

Vol 33 (4) ◽

pp. 665-666 ◽

Cited By ~ 11

Author(s):

A.R. Clarke

Keyword(s):

Cell Fate ◽

Gene Function ◽

Transcriptional Activation ◽

Underlying Disease ◽

Loss Of Function ◽

Critical Determinant ◽

Proliferation And Apoptosis ◽

Intestinal Tumour ◽

Early Effects ◽

Tumour Initiation

The use of mouse models to study neoplasia is proving particularly powerful in dissecting the mechanisms underlying disease initiation and progression. However, the majority of these models have been somewhat limited in studying the very early effects of loss of gene function, as tumour initiation relies upon either constitutive loss of gene function or spontaneous somatic loss of function. We have therefore adopted a strategy of using an inducible Cre-lox-based system to analyse the effects of loss of gene function, the use of which is reviewed here for the intestinal tumour suppressor APC (adenomatous polyposis coli). Using this approach, we have conditionally and synchronously inactivated APC in virtually all the epithelial cells of the adult murine small intestine. After 5 days following induction of Cre-mediated recombination, mice show grossly altered crypt/villus architecture. Deficiency in APC perturbs migration, alters the normal programme of differentiation and results in increased proliferation and apoptosis. Microarray analysis reveals the transcriptome to be significantly altered; reflecting both gross phenotypic changes and changes in transcriptional activation. These findings demonstrate that APC is indeed the critical determinant of cell fate in the intestinal epithelium, explaining its role as the cellular ‘gatekeeper’ in preventing neoplasia.

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Radiation Desiccation Response Motif-Like Sequences Are Involved in Transcriptional Activation of the Deinococcal ssb Gene by Ionizing Radiation but Not by Desiccation

Journal of Bacteriology ◽

10.1128/jb.00752-10 ◽

2010 ◽

Vol 192 (21) ◽

pp. 5637-5644 ◽

Cited By ~ 15

Author(s):

Aman Kumar Ujaoney ◽

Akhilesh A. Potnis ◽

Pratiksha Kane ◽

Rita Mukhopadhyaya ◽

Shree Kumar Apte

Keyword(s):

Mitomycin C ◽

Gamma Rays ◽

Transcriptional Activation ◽

Promoter Region ◽

Deinococcus Radiodurans ◽

Dna Binding Protein ◽

Similar Sequence ◽

Reading Frame ◽

Transcriptional Induction ◽

Transcriptional Fusions

ABSTRACT Single-stranded-DNA binding protein (SSB) levels during poststress recovery of Deinococcus radiodurans were significantly enhanced by 60Co gamma rays or mitomycin C treatment but not by exposure to UV rays, hydrogen peroxide (H2O2), or desiccation. Addition of rifampin prior to postirradiation recovery blocked such induction. In silico analysis of the ssb promoter region revealed a 17-bp palindromic radiation/desiccation response motif (RDRM1) at bp −114 to −98 and a somewhat similar sequence (RDRM2) at bp −213 to −197, upstream of the ssb open reading frame. Involvement of these cis elements in radiation-responsive ssb gene expression was assessed by constructing transcriptional fusions of edited versions of the ssb promoter region with a nonspecific acid phosphatase encoding reporter gene, phoN. Recombinant D. radiodurans strains carrying such constructs clearly revealed (i) transcriptional induction of the ssb promoter upon irradiation and mitomycin C treatment but not upon UV or H2O2 treatment and (ii) involvement of both RDRM-like sequences in such activation of SSB expression, in an additive manner.

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Time-Qualified Patterns of Variation of PPARγ, DNMT1, and DNMT3B Expression in Pancreatic Cancer Cell Lines

PPAR Research ◽

10.1155/2012/890875 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Valerio Pazienza ◽

Francesca Tavano ◽

Massimo Francavilla ◽

Andrea Fontana ◽

Fabio Pellegrini ◽

...

Keyword(s):

Pancreatic Cancer ◽

Cell Fate ◽

Cell Lines ◽

Expression Profiles ◽

Dna Methyltransferases ◽

Nutrient Sensing ◽

Cell Phenotype ◽

Peroxisome Proliferator ◽

Mrna Levels ◽

Peroxisome Proliferator Activated Receptors

Carcinogenesis is related to the loss of homeostatic control of cellular processes regulated by transcriptional circuits and epigenetic mechanisms. Among these, the activities of peroxisome proliferator-activated receptors (PPARs) and DNA methyltransferases (DNMTs) are crucial and intertwined. PPARγis a key regulator of cell fate, linking nutrient sensing to transcription processes, and its expression oscillates with circadian rhythmicity. Aim of our study was to assess the periodicity of PPARγand DNMTs in pancreatic cancer (PC). We investigated the time-related patterns ofPPARG, DNMT1, andDNMT3Bexpression monitoring their mRNA levels by qRT-PCR at different time points over a 28-hour span in BxPC-3, CFPAC-1, PANC-1, and MIAPaCa-2 PC cells after synchronization with serum shock.PPARGandDNMT1expression in PANC-1 cells andPPARGexpression in MIAPaCa-2 cells were characterized by a 24 h period oscillation, and a borderline significant rhythm was observed for thePPARG, DNMT1, andDNMT3Bexpression profiles in the other cell lines. The time-qualified profiles of gene expression showed different shapes and phase relationships in the PC cell lines examined. In conclusion,PPARGandDNMTsexpression is characterized by different time-qualified patterns in cell lines derived from human PC, and this heterogeneity could influence cell phenotype and human disease behaviour.

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