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her3, a zebrafish member of the hairy-E(spl) family, is repressed by Notch signalling.

her3 encodes a zebrafish bHLH protein of the Hairy-E(Spl) family. During embryogenesis, the gene is transcribed exclusively in the developing central nervous system, according to a fairly simple pattern that includes territories in the mesencephalon/rhombencephalon and the spinal cord. In all territories, the her3 transcription domain encompasses regions in which neurogenin 1 (neurog1) is not transcribed, suggesting regulatory interactions between the two genes. Indeed, injection of her3 mRNA leads to repression of neurog1 and to a reduction in the number of primary neurones, whereas her3 morpholino oligonucleotides cause ectopic expression of neurog1 in the rhombencephalon. Fusions of Her3 to the transactivation domain of VP16 and to the repression domain of Engrailed show that Her3 is indeed a transcriptional repressor. Dissection of the Her3 protein reveals two possible mechanisms for transcriptional repression: one mediated by the bHLH domain and the C-terminal WRPW tetrapeptide; and the other involving the N-terminal domain and the orange domain. Gel retardation assays suggest that the repression of neurog1 transcription occurs by binding of Her3 to specific DNA sequences in the neurog1 promoter. We have examined interrelationships of her3 with members of the Notch signalling pathway by the Gal4-UAS technique and mRNA injections. The results indicate that Her3 represses neurog1 and, probably as a consequence of the neurog1 repression, deltaA, deltaD and her4. Moreover, Her3 represses its own transcription as well. Surprisingly, and in sharp contrast to other members of the E(spl) gene family, transcription of her3 is repressed rather than activated by Notch signalling.

Animals↗

The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain.

The Drosophila morphogenetic protein Bicoid (Bcd) is a homeodomain-containing activator that stimulates the expression of target genes during early embryonic development. We demonstrate that a small domain of Bcd located immediately N-terminally of the homeodomain represses its own activity in Drosophila cells. This domain, referred to as a self-inhibitory domain, works as an independent module that does not rely on any other sequences of Bcd and can repress the activity of heterologous activators. We further show that this domain of Bcd does not affect its properties of DNA binding or subcellular distribution. A Bcd derivative with point mutations in the self-inhibitory domain severely affects pattern formation and target gene expression in Drosophila embryos. We also provide evidence to suggest that the action of the self-inhibitory domain requires a Drosophila co-factor(s), other than CtBP or dSAP18. Our results suggest that proper action of Bcd as a transcriptional activator and molecular morphogen during embryonic development is dependent on the downregulation of its own activity through an interaction with a novel co-repressor(s) or complex(es).

Alcohol Oxidoreductases↗

The central domain of Escherichia coli TyrR is responsible for hexamerization associated with tyrosine-mediated repression of gene expression.

TyrR from Escherichia coli regulates the expression of genes for aromatic amino acid uptake and biosynthesis. Its central ATP-hydrolyzing domain is similar to conserved domains of bacterial regulatory proteins that interact with RNA polymerase holoenzyme associated with the alternative sigma factor, sigma(54). It is also related to the common module of the AAA+ superfamily of proteins that is involved in a wide range of cellular activities. We expressed and purified two TyrR central domain polypeptides. The fragment comprising residues 188-467, called TyrR-(188-467), was soluble and stable, in contrast to that corresponding to the conserved core from residues 193 to 433. TyrR-(188-467) bound ATP and rhodamine-ATP with association constants 2- to 5-fold lower than TyrR and hydrolyzed ATP at five times the rate of TyrR. In contrast to TyrR, which is predominantly dimeric at protein concentrations less than 10 microm in the absence of ligands, or in the presence of ATP or tyrosine alone, TyrR-(188-467) is a monomer, even at high protein concentrations. Tyrosine in the presence of ATP or ATPgammaS promotes the oligomerization of TyrR-(188-467) to a hexamer. Tyrosine-dependent repression of gene transcription by TyrR therefore depends on ligand binding and hexamerization determinants located in the central domain polypeptide TyrR-(188-467).

Adenosine Triphosphatases↗

TopBP1 recruits Brg1/Brm to repress E2F1-induced apoptosis, a novel pRb-independent and E2F1-specific control for cell survival.

TopBP1 (DNA topoisomerase IIbeta binding protein I) contains multiple BRCT domains and is involved in replication and the DNA damage checkpoint. Through its BRCT domain, TopBP1 interacts with and represses exclusively E2F1 but not other E2F factors. This regulation of E2F1 transcriptional activity is mediated by a pRb-independent, but Brg1/Brm-dependent mechanism. TopBP1 recruits Brg1/Brm, a central component of the SWI/SNF chromatin-remodeling complex, to E2F1-responsive promoters and represses the activities of E2F1, but not E2F2 or E2F3. This regulation is crucial in the control of E2F1-dependent apoptosis during normal cell growth and DNA damage. Interestingly, TopBP1 is induced by E2F and interacts with E2F1 during G1/S transition. Thus, TopBP1 functions as a critical modulator and serves as a negative feedback regulator of E2F1 by inhibiting E2F1-dependent apoptosis during G1/S transition as well as DNA damage to promote cell survival.

Apoptosis↗

NF1/X represses PDGF A-chain transcription by interacting with Sp1 and antagonizing Sp1 occupancy of the promoter.

The regulatory mechanisms mediating basal and inducible platelet-derived growth factor (PDGF)-A expression have been the focus of intense recent investigation, but repression of PDGF-A expression is largely unexplored. Here we isolated a nuclear factor that interacts with the proximal region of the PDGF-A promoter using bulk binding assays and chromatography techniques. Peptide mass fingerprint and supershift analysis revealed this DNA-binding protein to be NF1/X. NF1/X repressed PDGF-A promoter-dependent transcription and endogenous mRNA expression, which was reversible by oligonucleotide decoys bearing an NF1/X-binding site. Mutation in the DNA-binding domain of NF1/X abolished its repression of PDGF-A promoter. NF1/X antagonized the activity of a known activator of the PDGF-A chain, Sp1, by inhibiting its occupancy of the proximal PDGF-A promoter. NF1/X physically and specifically interacts with Sp1 via its subtype-specific domain and blocks Sp1 induction of the promoter. NF1/X residues 311-416 mediated NF1/X suppression of basal PDGF-A transcription, whereas residues 243-416 were required for NF1/X repression of Sp1-inducible promoter activity. These findings demonstrate that repression of PDGF-A gene transcription is governed by interplay between NF1/X and Sp1.

Amino Acid Sequence↗

Vitamin D3: a transcriptional modulator of the interferon-gamma gene.

1Alpha,25-dihydroxyvitamin D3 [1,25-(OH)2D3] exerts several effects on the immune system, by regulating lymphocyte proliferation, differentiation of monocytes and secretion of cytokines as IL-2, granulocyte-macrophage colony-stimulating factor and IFN-gamma in T cells. Here, we analyze the effect of 1,25-(OH)2D3 on IFN-gamma gene transcription. Transient transfection assays in Jurkat T cells indicate that activation of the IFN-gamma promoter is down-regulated by 1,25-(OH)2D3. This effect is enhanced by retinoid X receptor (RXR), and a functional vitamin D3 receptor (VDR) DNA-binding domain in necessary for repression. We delineated two important promoter regions mainly involved in this modulation. The first of these is situated at the level of a promoter-silencer previously characterized and binds the heterodimer VDR-RXR in electrophoretic mobility shift assay. Residual negative regulation was also detected at the level of the promoter fragment -108 to +64 bp from the transcription start site and, surprisingly, the activity of the IFN-gamma enhancer from -108 to -36 bp in the context of a heterologous promoter was not affected by 1,25-(OH)2D3. Moreover, binding activity for VDR-RXR has been detected in the IFN-gamma minimal promoter, suggesting a possible mechanism of interference with transcription initiation/progression. The overall data indicate that direct modulation of the IFN-gamma promoter activity is one of the possible mechanisms involved in the repressive effect of 1,25-(OH)2D3 on IFN-gamma gene expression.

Animals↗

Do protein motifs read the histone code?

The existence of different patterns of chemical modifications (acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation) of the histone tails led, some years ago, to the histone code hypothesis. According to this hypothesis, these modifications would provide binding sites for proteins that can change the chromatin state to either active or repressed. Interestingly, some protein domains present in histone-modifying enzymes are known to interact with these covalent marks in the histone tails. This was first shown for the bromodomain, which was found to interact selectively with acetylated lysines at the histone tails. More recently, it has been described that the chromodomain can be targeted to methylation marks in histone N-terminal domains. Finally, the interaction between the SANT domain and histones is also well documented. Overall, experimental evidence suggests that these domains could be involved in the recruitment of histone-modifying enzymes to discrete chromosomal locations, and/or in the regulation their enzymatic activity. Within this context, we review the distribution of bromodomains, chromodomains and SANT domains among chromatin-modifying enzymes and discuss how they can contribute to the translation of the histone code.

Adenosine Triphosphate↗

Long-range silencing and position effects at telomeres and centromeres: parallels and differences.

Most of the human genome is compacted into heterochromatin, a form that encompasses multiple forms of inactive chromatin structure. Transcriptional silencing mechanisms in budding and fission yeasts have provided genetically tractable models for understanding heritably repressed chromatin. These silent domains are typically found in regions of repetitive DNA, that is, either adjacent to centromeres or telomeres or within the tandemly repeated ribosomal DNA array. Here we address the mechanisms of centromeric, telomeric and locus-specific gene silencing, comparing simple and complex animals with yeast. Some aspects are universally shared, such as histone-tail modifications, while others are unique to either centromeres or telomeres. These may reflect roles for heterochromatin in other chromosomal functions, like kinetochore attachment and DNA ends protection.

Animals↗

Dominant negative retinoic acid receptor beta.

Induction of the retinoic acid receptor beta 2 (RAR beta 2) gene by retinoic acid (RA) is mediated by a RA response element (RARE), which represents a high affinity binding site for RAR/RXR heterodimers acting at this site as RA-inducible transcription activators. In RA resistant RAC65 cells, RAR beta 2 induction is blocked due to expression of a truncated RAR alpha acting as a dominant negative repressor. Here we show that exogenous expression of RAR but not RXR can restore RA-dependent RAR beta 2 promoter activation in RAC65 cells. Structure-function analysis of hRAR beta 2 mutants in RAC65 cells shows, that the transactivation function required to restore RAR beta 2 promoter activation is dependent on the DNA binding, dimerization and RA-dependent transactivation properties of hRAR beta 2, which are retained in a mutant (beta delta 409) lacking the F domain. By contrast, dominant repression of RA-dependent mRAR beta 2 promoter activation by hRAR beta 2 mutants is independent of the DNA binding or RA-dependent transactivation function but requires a region (residues 204-384) in hRAR beta 2 involved in heterodimerization with RXR. These data extend previous observations on structure-function of RARs and provides tools for studying the role of retinoids and RARs during vertebrate development.

Amino Acid Sequence↗

A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes.

The stripe pattern of pair rule gene expression along the anterior-posterior axis of the Drosophila blastoderm embryo represents the first sign of periodicity during the process of segmentation. Striped gene expression can be mediated by distinct cis-acting elements that give rise to individual stripe expression domains in direct response to maternal and first zygotic factors. Here we show that the expression of stripes can also be generated by a different, two-step mode which involves regulatory interactions among the primary pair rule genes hairy (h) and runt (run). Expression of h stripes 3 and 4 is directed by a common cis-acting element that results in an initial broad band of gene expression covering three stripe equivalents. Subsequently, this expression domain is split by repression in the forthcoming interstripe region, a process mediated by a separate cis-acting element that responds to run activity. This second mode of pair rule stripe formation may have evolutionary implications.

Animals↗

DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG.

DNA methylation is interpreted by a family of methyl-CpG binding domain (MBD) proteins that repress transcription through recruitment of corepressors that modify chromatin. To compare in vivo binding of MeCP2 and MBD2, we analyzed immunoprecipitated chromatin from primary human cells. Genomic sites occupied by the two MBD proteins were mutually exclusive. As MeCP2 was unable to colonize sites vacated by depletion of MBD2, we tested the hypothesis that methyl-CpG alone is insufficient to direct MeCP2 binding. In vitro selection for MeCP2 bound DNA-enriched fragments containing A/T bases ([A/T] > or = 4) adjacent to methyl-CpG. [A/T] > or = 4 was found to be essential for high-affinity binding at selected sites and at known MeCP2 target regions in the Bdnf and Dlx6 genes. MBD2 binding, however, did not require an A/T run. The unexpected restriction of MeCP2 to a defined subset of methyl-CpG sites will facilitate identification of genomic targets that are relevant to Rett Syndrome.

Adenine↗

Isolation of a cDNA encoding a widely expressed novel zinc finger protein with the LeR and KRAB-A domains.

We have isolated a human cDNA clone representing a novel human gene. The predicted 683-amino-acid protein, designated FPM315, contains nine C2H2-type zinc finger motifs and two regions homologous to the LeR domain, a finger-associated structural domain, and the A element of the Kruppel-associated box (KRAB) domain involved in transcriptional repression. The FPM315 mRNAs were expressed in all human tissues so far examined. A cross-species genomic hybridization indicates that the FPM315 gene is highly conserved among eukaryotes. These data suggest that FPM315 might play an important role in basic cellular processes.

Amino Acid Sequence↗

HpEts, an ets-related transcription factor implicated in primary mesenchyme cell differentiation in the sea urchin embryo.

The mechanism of micromere specification is one of the central issues in sea urchin development. In this study we have identified a sea urchin homologue of ets 1 + 2. HpEts, which is maternally expressed ubiquitously during the cleavage stage and which expression becomes restricted to the skeletogenic primary mesenchyme cells (PMC) after the hatching blastula stage. The overexpression of HpEts by mRNA injection into fertilized eggs alters the cell fate of non-PMC to migratory PMC. HpEts induces the expression of a PMC-specific spicule matrix protein, SM50, but suppresses of aboral ectoderm-specific arylsulfatase and endoderm-specific HpEndo16. The overexpression of dominant negative delta HpEts which lacks the N terminal domain, in contrast, specifically represses SM50 expression and development of the spicule. In the upstream region of the SM50 gene there exists an ets binding site that functions as a positive cis-regulatory element. The results suggest that HpEts plays a key role in the differentiation of PMCs in sea urchin embryogenesis.

Amino Acid Sequence↗

p53- and Mdm2-independent repression of NF-kappa B transactivation by the ARF tumor suppressor.

One mechanism by which a cell affords protection from the transforming effects of oncogenes is via the action of the tumor suppressor, ARF, which activates p53 by inactivating Mdm2. Many oncogenes have also been shown to activate the transcription factor NF-kappa B, which can contribute toward the malignant phenotype in many ways, including an ability to antagonize p53. Here we find that ARF inhibits NF-kappa B function and its antiapoptotic activity independent of Mdm2 and p53. ARF represses the transcriptional activation domain of the NF-kappa B family member RelA by inducing its association with the histone deacetylase, HDAC1. Further, we show that the response of NF-kappa B to the oncogene Bcr-Abl is determined by the ARF status of the cell. These results reveal an important function of ARF that can regulate the NF-kappa B response to oncogene activation.

Cell Transformation, Neoplastic↗

When negative is positive in functional genomics.

The post-genomic era has caused classical approaches to analyse gene function to be reviewed and refined. Conventional reverse genetic approaches to predict gene function have drawbacks in terms of genetic redundancy and being limited mainly to well-characterized genomes. The relatively recent use of dominant-negative transgenes has been successful in elaborating certain pathways and it is now possible to extend this technique to convert transcription factors into dominant repressor functions by fusion to repressor domains such as ENGRAILED from Drosophila. This methodology opens up new possibilities to overcome genetic redundancy, to identify novel gene functions and also to apply information on conserved protein domains between species to repress heterologous protein function.

Animals↗

Mutual repression of transcriptional activation between the ETS-related factor ERG and estrogen receptor.

Transcription factors are known to interact with each other to modulate their transcriptional activity. In this study, we found that the transcriptional activity of human Erg (one of the Ets family-transcription factors) was repressed by several nuclear receptors, including human estrogen receptor ERalpha, nonsteroid receptors and orphan receptors. Conversely, Erg inhibited ERalpha-dependent transcription. These reciprocal functional interactions extended to other nuclear receptors such as thyroid hormone and retinoic acid receptors, as well as to Fli1, an ERG-related ETS factor. Although similarly inhibited by overexpression of the orphan nuclear receptors ERR1 and RORalpha, ERG activity was unaffected by either REV-ERBalpha1 or COUP-TFII. The antagonism between ERG and ERalpha did not depend on DNA binding inhibition or direct protein-protein interactions. Repression of ERalpha-dependent transcription required the carboxyterminal and aminoterminal transactivation domains of Erg whereas the carboxyterminal AF-2 domain of ERalpha was necessary for repression of Erg activity. Reciprocal inhibition between Erg and ERalpha was not alleviated by overexpressing CBP, SRC-1 or RIP 140, three nuclear coactivator proteins. A negative cross-talk observed between Erg and ERalpha expands their potential range of regulation and may be relevant in vivo, particularly in endothelial, urogenital and cartilaginous tissues where both factors are expressed.

Animals↗

Identification of cyclin A/Cdk2 phosphorylation sites in B-Myb.

B-myb is a highly conserved member of the myb proto-oncogene family that encodes a ubiquitously expressed 110-kDa sequence-specific DNA-binding protein. Transactivation of Myb-inducible promoters by B-Myb is repressed by a regulatory domain located at the C-terminus of the protein. Cyclin A/Cdk2-mediated phosphorylation apparently releases the negative constraint and triggers B-Myb transactivation potential. Two-dimensional tryptic phosphopeptide analysis indicated that the majority of the sites phosphorylated in vivo are targeted in vitro by cyclin A/Cdk2. Six sites in B-Myb fulfil the requirements for recognition by Cdk2. Using point mutation of the phosphorylation sites to nonphosphorylatable amino acids, we show that five of these sites are targets for Cdk2 in vivo. Mutation of one of these residues (T524) to alanine diminished the ability of B-Myb to promote transcription of a reporter gene, suggesting that phosphorylation of B-Myb at this site is important for the regulation of its activity by cyclin A/Cdk2.

Amino Acid Substitution↗

Leucine-zipper dimerization motif encoded by the AF17 gene fused to ALL-1 (MLL) in acute leukemia.

Chromosome region 11q23 is involved in reciprocal chromosome translocations associated with human acute leukemias. These aberrations fuse the ALL-1 gene located at 11q23 to a series of partner genes positioned on a variety of human chromosomes. The fused genes encode chimeric proteins. Here we report the cloning and characterization of the ALL-1 partner at 17q21, the AF17 gene. The AF17 gene encodes a protein of 1093 amino acids, containing a leucine-zipper dimerization motif located 3' of the fusion point and a cysteine-rich domain at the N terminus. The latter can be arranged in three zinc fingers and shows homology to a domain within the protein Br140 (peregrin). AF17 contains stretches of amino acids previously associated with domains involved in transcriptional repression or activation. Based on features of AF17 and of the proteins encoded by the other partner genes analyzed and in conjunction with other recent studies, we propose a model in which ALL-1 rearrangements result in loss of function of the gene. In this model, the partner polypeptide plays an accessory role either by repressing activity of the truncated ALL-1 protein or by blocking the function of the normal protein presumably present in the leukemic cells.

Amino Acid Sequence↗