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BMP7 is a morphogen capable of counteracting the OA chondrocyte hypertrophic phenotype via NKX3-2. NKX3-2 represses expression of RUNX2, an important transcription factor for chondrocyte hypertrophy. Since RUNX2 has previously been described as an inhibitor for 47S pre-rRNA transcription, we hypothesized that BMP7 positively influences 47S pre-rRNA transcription through NKX3-2, resulting in increased protein translational capacity. Therefor SW1353 cells and human primary chondrocytes were exposed to BMP7 and rRNA (18S, 5.8S, 28S) expression was determined by RT-qPCR. NKX3-2 knockdown was achieved via transfection of a NKX3-2-specific siRNA duplex. Translational capacity was assessed by the SUNsET assay, and 47S pre-rRNA transcription was determined by transfection of a 47S gene promoter-reporter plasmid. BMP7 treatment increased protein translational capacity. This was associated by increased 18S and 5.8S rRNA and NKX3-2 mRNA expression, as well as increased 47S gene promotor activity. Knockdown of NKX3-2 led to increased expression of RUNX2, accompanied by decreased 47S gene promotor activity and rRNA expression, an effect BMP7 was unable to restore. Our data demonstrate that BMP7 positively influences protein translation capacity of SW1353 cells and chondrocytes. This is likely caused by an NKX3-2-dependent activation of 47S gene promotor activity. This finding connects morphogen-mediated changes in cellular differentiation to an aspect of ribosome biogenesis via key transcription factors central to determining the chondrocyte phenotype.

Changes in gene regulation during differentiation are governed by networks of transcription factors. The Arabidopsis root endodermis is a tractable model to address how transcription factors contribute to differentiation. We used a bottom-up approach to understand the extent to which transcription factors that are required for endodermis differentiation can confer endodermis identity to a non-native cell type. Our results show that the transcription factors SHORTROOT and MYB36 alone have limited ability to induce ectopic endodermal features in the absence of additional cues. The stele-derived signalling peptide CIF2 stabilizes SHORTROOT-induced endodermis identity acquisition. The outcome is a partially impermeable barrier deposited in the subepidermal cell layer, which has a transcriptional signature similar to the endodermis. These results demonstrate that other root cell types can be forced to differentiate into the endodermis and highlight a previously unappreciated role for receptor kinase signalling in maintaining endodermis identity.

HCF-2 is a member of thehost-cell-factor protein family, which arose in early vertebrate evolution as a result of gene duplication. Whereas its paralog, HCF-1, is known to act as a versatile chromatin-associated protein required for cell proliferation and differentiation, much less is known about HCF-2. Here, we show that HCF-2 is broadly present in human and mouse cells, and possesses activities distinct from HCF-1. Unlike HCF-1, which is excluded from nucleoli, HCF-2 is nucleolar — an activity conferred by one and a half C-terminal Fibronectin type 3 repeats and inhibited by the HCF-1 nuclear localization signal. Elevated HCF-2 synthesis in HEK-293 cells results in phenotypes reminiscent of HCF-1-depleted cells, including inhibition of cell proliferation and mitotic defects. Furthermore, increased HCF-2 levels in HEK-293 cells lead to inhibition of cell proliferation and metabolism gene-expression programs with parallel activation of differentiation and morphogenesis gene-expression programs. Thus, the HCF ancestor appears to have evolved into a small two-member protein family possessing contrasting nuclear vs. nucleolar localization, and cell proliferation and differentiation functions.

Matrix metalloproteinase 2 (MMP-2) is a metalloproteinase belonging to a family of structurally related zinc-dependent endopeptidases capable of degrading extracellular matrix components. To elucidate the functional promoter of the mouse MMP-2 gene, systematic transient expression analysis of the 5'-flanking region of the MMP-2 gene was performed using serially nested deletions. The deletion analysis indicated that the proximal 327-bp sequence from nucleotide positions -313 to +14 relative to the transcription start site is essential for minimal promoter activity and that a 10-bp sequence of the promoter at positions -939 to -930 is required for high expression level of the MMP-2 gene. The 10-bp fragment functioned as a potent stimulator of heterologous SV40 promoter activity. This element is identical to the YB-1 binding motif (Y-box) present within the responsive element-1 (RE-1), which has been shown to act as a potent cis-activator of transcription of the rat MMP-2 gene. The binding of a nuclear factor(s) to the 10-bp fragment was also revealed by electrophoretic mobility shift assays (EMSAs). Antibody-supershift EMSAs of nuclear extracts from NIH 3T3 cells demonstrated YB-1 binding to the RE-1 sequence. It was concluded that the RE-1 is the conserved element for potent expression of MMP-2 gene among rodents.

International audience; The Ccr4-Not complex is a conserved global regulator of gene expression, which serves as a regulatory platform that senses and/or transmits nutrient and stress signals to various downstream effectors. Presumed effectors of this complex in yeast are TFIID, a general transcription factor that associates with the core promoter, and Msn2, a key transcription factor that regulates expression of stress-responsive element (STRE)-controlled genes. Here we show that the constitutively high level of STRE-driven expression in ccr4-not mutants results from two independent effects. Accordingly, loss of Ccr4-Not function causes a dramatic Msn2-independent redistribution of TFIID on promoters with a particular bias for STRE-controlled over ribosomal protein gene promoters. In parallel, loss of Ccr4-Not complex function results in an alteration of the post-translational modification status of Msn2, which depends on the type 1 protein phosphatase Glc7 and its newly identified subunit Bud14. Tests of epistasis as well as transcriptional analyses of Bud14-dependent transcription support a model in which the Ccr4-Not complex prevents activation of Msn2 via inhibition of the Bud14/Glc7 module in exponentially growing cells. Thus, increased activity of STRE genes in ccr4-not mutants may result from both altered general distribution of TFIID and unscheduled activation of Msn2.

Pax6 transcription factor is required for islet cell number, morphology, and hormone gene expression. The perinatal lethality of Pax6 null mutants has restricted investigation of the role of Pax6 in normal endocrine cell function. Therefore, we devised the conditional inactivation of Pax6 using the Pdx1 and Pax6 regulatory domains to activate Cre in cells of either the entire pancreatic bud or only in endocrine cell lineages, respectively. Mutant pups died few days after birth, suffering from an overt diabetic phenotype that includes hyperglycemia, hypoinsulinemia, weight loss, and ketosis, indicating an essential role for Pax6 in beta cell function. Glucose-transporter type-2 expression was downregulated, but expression of several transcription factors essential for endocrine development was maintained. Our findings support a role for Pax6 activity in maintaining normal beta cell function after birth, but not for beta cell neogenesis during late embryonic development and early postnatal stages.

Interleukin-1 (IL-1) costimulation is required for efficient IL-2 synthesis and IL-2 receptor (IL-2R) expression of T cells. The molecular events leading to these effects are largely unknown. We utilized an IL-1-responsive and an IL-1-non-responsive subclone of the mouse thymoma cell line EL4 to investigate how IL-1 activates IL-2 gene expression. We correlated IL-2 promoter activity with the activity of the endogenous IL-2 gene, thereby showing the biological significance of our results. Our experiments provide new functional data showing that a major target of IL-1 mediated costimulation is the chi B-like site, T cell element distal TCEd (GGGATTTCAC), of the IL-2 promoter. Thus, deletion or mutation of TCEd within a complete IL-2 promoter abrogated IL-1 costimulation in the IL-1 responsive EL4 subclone. Therefore, the TCEd element is functionally essential for the effect of IL-1. We also identified a nuclear factor (NF), IL-1 NF, that binds to the TCEd site after IL-1 stimulation. This factor was only present in the IL-1-responsive EL4 subclone and not in the IL-1-non-responsive subclone after IL-1 stimulation and did not appear after phytohemagglutinin (PHA)-treatment. Binding of IL-1 NF to the TCEd site was competed by a typical chi B oligonucleotide, suggesting that it is similar to NF-chi B in its DNA-binding properties. However, the TCEd element was only activated by costimulation with PHA and IL-1 whereas a typical chi B element was already activated by IL-1 alone. These data suggest that the biological function of the TCEd element of the IL-2 promoter differs from that of a canonical chi B element. Our data provide new evidence that IL-1 acts on the IL-2 promoter by activating the TCEd element via the transcription factor IL-1 NF. Furthermore, activation of this element requires two signals, delivered by IL-1 and PHA, in this way reflecting the activation requirement for the endogenous IL-2 gene.

Repeated exposure to opiates leads to cellular and molecular changes and behavioral alterations reflecting a state of dependence. In noradrenergic neurons, cyclic AMP (cAMP)-dependent pathways are activated during opiate withdrawal, but their contribution to the activity of locus coeruleus noradrenergic neurons and behavioral manifestations remains controversial. Here, we test whether the cAMP-dependent transcription factors cAMP responsive element binding protein (CREB) and cAMP-responsive element modulator (CREM) in noradrenergic neurons control the cellular markers and the physical signs of morphine withdrawal in mice. Using the Cre/loxP system we ablated the Creb1 gene in noradrenergic neurons. To avoid adaptive effects because of compensatory up-regulation of CREM, we crossed the conditional Creb1 mutant mice with a Crem-/- line. We found that the enhanced expression of tyrosine hydroxylase normally observed during withdrawal was attenuated in CREB/CREM mutants. Moreover, the withdrawal-associated cellular hyperactivity and c-fos expression was blunted. In contrast, naloxone-precipitated withdrawal signs, such as jumping, paw tremor, tremor and mastication were preserved. We conclude by a specific genetic approach that the withdrawal-associated hyperexcitability of noradrenergic neurons depends on CREB/CREM activity in these neurons, but does not mediate several behavioral signs of morphine withdrawal.

The conserved multi-subunit Ccr4-Not complex regulates gene expression in diverse ways. In this work, we characterize the suppression of temperature sensitivity associated with a mutation in the gene encoding the scaffold subunit of the Ccr4-Not complex, NOT1, by the deletion of SPT3. We determine that the deletion of SPT3, but not the deletion of genes encoding other subunits of the SAGA complex, globally suppresses transcriptional defects of not1-2. We find that transcriptional activation in not1-2 is associated with increased binding of TFIID and SAGA at promoters of upregulated genes, and this is suppressed by the deletion of SPT3. Interestingly, Spt3p-dependent activation of transcription occurs in not1-2 even if the SAGA complex is disrupted by the deletion of SPT7 that encodes a subunit of SAGA required for its integrity. Consistent with a SAGA-independent function of Spt3p, the deletion of SPT3 displays synthetic phenotypes when combined with a deletion of SPT7. Taken together, our results provide a new view of the Spt3 protein by identifying a SAGA-independent function of this protein that is functionally linked to the Ccr4-Not complex.

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such “localizome” maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated “version 1.1” of the Promoterome: a resource of ∼6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources (promoter::ORF::GFP).

Plants have evolved protective mechanisms to ensure their survival when threatened by adverse environmental conditions during their transition to autotrophic growth. During germination, there is a 2- to 3-d period during which a plant can execute growth arrest when challenged by water deficit. This postgermination developmental checkpoint is signaled by the stress hormone abscisic acid (ABA), which induces the expression of the bZIP transcription activator ABI5. The growth arrest efficiency depends on ABI5 levels, andabi5mutants are ABA-insensitive and unable to execute the ABA-mediated growth arrest. Here we show that a novel ABI5-interacting protein, designated as AFP, can form high molecular weight (Mr) complexes with ABI5 in embryo-derived extracts. LikeABI5,ABI five binding protein(AFP) mRNA and protein levels are induced by ABA during seed germination. Two differentafpmutant alleles (afp-1andafp-2) are hypersensitive to ABA, whereas transgenic plants overexpressing AFP are resistant; in these plants, AFP and ABI5 protein levels are inversely correlated. Genetic analysis shows thatabi5-4is epistatic toafp-1, indicating the ABA hypersensitivity ofafpmutants requires ABI5. Proteasome inhibitor studies show that ABI5 stability is regulated by ABA through ubiquitin-related events. When expressed together, AFP and ABI5 are colocalized in nuclear bodies, which also contain COP1, a RING motif protein. Our results suggest that AFP attenuates ABA signals by targeting ABI5 for ubiquitin-mediated degradation in nuclear bodies.

Metals are necessary for the normal functioning of cells and the survival of organisms. However, exposure to higher than the physiological levels of several metals may lead to tumor development. Although the exact molecular mechanism(s) of metal-induced carcinogenesis is not clear, a vast body of evidence indicates that metal-induced generation of reactive oxygen species (ROS) may play a central role in this process. Two main pathways of ROS-induced effects are discussed in this chapter: (i) increased DNA damage induced either directly or indirectly by impeding DNA repair, and (ii) modulation of nuclear transcriptional factor activities, such as NF-kappaB and AP-1, through mitogen-activated protein kinases signal transduction mechanisms. Crit Rev Oncol Hematol

NC2 is a heterodimeric regulator of transcription that plays both positive and negative roles in vivo. Here we show that the alpha and beta subunits of yeast NC2 are not always associated in a tight complex. Rather, their association is regulated, in particular by glucose depletion. Indeed, stable NC2 alpha/beta complexes can only be purified from cells after the diauxic shift when glucose has been depleted from the growth medium. In vivo, the presence of NC2 alpha, but not NC2 beta, at promoters generally correlates with the presence of TBP and transcriptional activity. In contrast, increased presence of NC2 beta relative to TBP correlates with transcriptional repression. NC2 is regulated by phosphorylation. We found that mutation of genes encoding casein kinase II (CKII) subunits as well as potential CKII phosphorylation sites in NC2 alpha and beta affected gene repression. Interestingly, NC2-dependent repression in the phosphorylation site mutants was only perturbed in high glucose when NC2 beta and NC2 alpha are not associated, but not after the diauxic shift when NC2 alpha and beta form stable complexes. Thus, the separation of NC2 alpha and beta function indicated by these mutants also supports the existence of multiple NC2 complexes with different functions in transcription.

Genetic experiments in the yeast Saccharomyces cerevisiae have identified the five Not proteins as global repressors of transcription which preferentially repress core promoters which do not contain a canonical TATA sequence. Recently, the Ccr4 and Caf1 proteins, required for non-fermentative gene expression, were found to be associated with the five Not proteins in 1.2 and 2 MDa Ccr4-Not complexes. These Ccr4-Not complexes, as many other global regulators of transcription, appear to regulate transcription both positively and negatively in vivo. To further characterize the activity of Not1p, the only essential known protein of the Ccr4-Not complex, and determine whether it can act directly as a transcriptional repressor, we established an in vitro transcription system in which the HIS3 TATA-less promoter can be efficiently transcribed. We demonstrate that transcription from the HIS3 TATA-less promoter can be specifically increased in vitro by preparing nuclear extracts from a conditional mutant of the NOT1 gene and analyzing transcription after shifting the nuclear extracts to the restrictive temperature. This result is the first demonstration that one of the Not proteins directly represses transcription. Moreover, it now defines an experimental system in which TATA-less transcription initiation and repression by the Ccr4-Not complex can be studied further.

Steroid hormones are essential for normal sexual development, accommodation to stress, and regulation of fluid and electrolyte balance. Biosynthesis of these different classes of steroids and its appropriate regulation requires the precisely controlled expression of six different cytochrome P-450 enzymes and two hydroxysteroid dehydrogenases in different tissues. The molecular mechanism of the tissue-specific and pituitary hormone-regulated expression of the genes encoding P-450 enzymes in the steroidogenic tissues is the central problem of long-term regulation of steroidogenesis. Orphan members of the nuclear receptor superfamily play an important role in mediating transcriptional regulation of several steroid hydroxylase genes. Two of these transcription factors, steroidogenic factor-1 (SF-1) and DAX-1, will be reviewed here in detail.

There is growing evidence that Gli proteins participate in the mediation of Hedgehog and FGF signaling in neural and mesodermal development. However, little is known about which genes act downstream of Gli proteins. Here we show the regulation of members of the Wnt family by Gli proteins in different contexts. Our findings indicate that Gli2 regulates Wnt8 expression in the ventral marginal zone of the early frog embryo: activating Gli2 constructs induce ectopic Wnt8 expression in animal cap explants, whereas repressor forms inhibit its endogenous expression in the marginal zone. Using truncated Frizzled and dominant-negative Wnt constructs, we then show the requirement of at least two Wnt proteins, Wnt8 and Wnt11, for Gli2/3-induced posterior mesodermal development. Blocking Wnt signals, however, inhibits Gli2/3-induced morphogenesis, but not mesodermal specification. Gli2/3 may therefore normally coordinate the action of these two Wnt proteins, which regulate distinct downstream pathways. In addition, the finding that Gli1 consistently induces a distinct set of Wnt genes in animal cap explants and in skin tumors suggests that Wnt regulation by Gli proteins is general. Such a mechanism may link signals that induce Gli activity, such as FGFs and Hedgehogs, with Wnt function.

Environmental chemicals with estrogenic activities have been suggested to be associated with deleterious effects in animals and humans. To characterize estrogenic chemicals and their mechanisms of action, we established in vitro and cell culture assays that detect human estrogen receptor [alpha] (hER[alpha])-mediated estrogenicity. First, we assayed chemicals to determine their ability to modulate direct interaction between the hER[alpha] and the steroid receptor coactivator-1 (SRC-1) and in a competition binding assay to displace 17ss-estradiol (E(2)). Second, we tested the chemicals for estrogen-associated transcriptional activity in the yeast estrogen screen and in the estrogen-responsive MCF-7 human breast cancer cell line. The chemicals investigated in this study were o,p'-DDT (racemic mixture and enantiomers), nonylphenol mixture (NPm), and two poorly analyzed compounds in the environment, namely, tris-4-(chlorophenyl)methane (Tris-H) and tris-4-(chlorophenyl)methanol (Tris-OH). In both yeast and MCF-7 cells, we determined estrogenic activity via the estrogen receptor (ER) for o,p'-DDT, NPm, and for the very first time, Tris-H and Tris-OH. However, unlike estrogens, none of these xenobiotics seemed to be able to induce ER/SRC-1 interactions, most likely because the conformation of the activated receptor would not allow direct contacts with this coactivator. However, these compounds were able to inhibit [(3)H]-E(2) binding to hER, which reveals a direct interaction with the receptor. In conclusion, the test compounds are estrogen mimics, but their molecular mechanism of action appears to be different from that of the natural hormone as revealed by the receptor/coactivator interaction analysis. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8