Characterization of CD34+ Cells from Patients with Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) Using a t-Distributed Stochastic Neighbor Embedding (t-SNE) Protocol

Using multi-color flow cytometry analysis, we studied the immunophenotypical differences between leukemic cells from patients with AML/MDS and hematopoietic stem and progenitor cells (HSPCs) from patients in complete remission (CR) following their successful treatment. The panel of markers included CD34, CD38, CD45RA, CD123 as representatives for a hierarchical hematopoietic stem and progenitor cell (HSPC) classification as well as programmed death ligand 1 (PD-L1). Rather than restricting the evaluation on a 2- or 3-dimensional analysis, we applied a t-distributed stochastic neighbor embedding (t-SNE) approach to obtain deeper insight and segregation between leukemic cells and normal HPSCs. For that purpose, we created a t-SNE map, which resulted in the visualization of 27 cell clusters based on their similarity concerning the composition and intensity of antigen expression. Two of these clusters were "leukemia-related" containing a great proportion of CD34+/CD38- hematopoietic stem cells (HSCs) or CD34+ cells with a strong co-expression of CD45RA/CD123, respectively. CD34+ cells within the latter cluster were also highly positive for PD-L1 reflecting their immunosuppressive capacity. Beyond this proof of principle study, the inclusion of additional markers will be helpful to refine the differentiation between normal HSPCs and leukemic cells, particularly in the context of minimal disease detection and antigen-targeted therapeutic interventions. Furthermore, we suggest a protocol for the assignment of new cell ensembles in quantitative terms, via a numerical value, the Pearson coefficient, based on a similarity comparison of the t-SNE pattern with a reference.

Identification of nanoparticles as vesicular cargo via Airy scanning fluorescence microscopy and spatial statistics

Many biomedical applications of nanoparticles on the cellular level require a characterisation of their subcellular distribution. Depending on the nanoparticle and its preferred intracellular compartment, this may be a nontrivial task, and consequently, the available methodologies are constantly increasing. Here, we show that super-resolution microscopy in combination with spatial statistics (SMSS), comprising the pair correlation and the nearest neighbour function, is a powerful tool to identify spatial correlations between nanoparticles and moving vesicles. Furthermore, various types of motion like for example diffusive, active or Lévy flight transport can be distinguished within this concept via suitable statistical functions, which also contain information about the factors limiting the motion, as well as regarding characteristic length scales. The SMSS concept fills a methodological gap related to mobile intracellular nanoparticle hosts and its extension to further scenarios is straightforward. It is exemplified on MCF-7 cells after exposure to carbon nanodots, demonstrating that these particles are stored predominantly in the lysosomes.

Uptake of carbon nanodots into human AML cells in comparison to primary hematopoietic cells

Carbon nanodots (CNDs) comprise a class of next generation nanomaterials with a wide variety of potential applications. Here, we report on their uptake into primary hematopoietic cells from three normal donors and malignant cells from five patients with de novo acute myeloid leukemia (AML). A significant CND uptake was observed in all cell types of the normal and leukemic cells. Still, the uptake was significantly smaller for the CD34⁺ and CD33⁺ myeloid subsets of the malignant cell population as compared to the normal blood-derived CD34⁺ and CD33⁺ cells. For the T and B lymphoid cell populations as defined by CD3 and CD19 within the leukemic and normal samples a similar uptake was observed. The CNDs accumulate preferentially in small clusters in the periphery of the nucleus as already shown in previous studies for CD34⁺ progenitor/stem cells and human breast cancer cells. This particular subcellular localization could be useful for targeting the lysosomal compartment, which plays a pivotal role in the context of autophagy associated survival of AML cells. Our results demonstrate the usability of CNDs beyond their application for in vitro and in vivo fluorescence labeling or drug delivery into normal and malignant cells.

Carbon nanodots (CNDs) comprise a class of next generation nanomaterials with a wide variety of potential applications.

From in vitro to ex vivo: subcellular localization and uptake of graphene quantum dots into solid tumors

Among various nanoparticles tested for pharmacological applications over the recent years, graphene quantum dots (GQDs) seem to be promising candidates for the construction of drug delivery systems due to their superior biophysical and biochemical properties. The subcellular fate of incorporated nanomaterial is decisive for transporting pharmaceuticals into target cells. Therefore a detailed characterization of the uptake of GQDs into different breast cancer models was performed. The demonstrated accumulation inside the endolysosomal system might be the reason for the particles' low toxicity, but has to be overcome for cytosolic or nuclear drug delivery. Furthermore, the penetration of GQDs into precision-cut mammary tumor slices was studied. These constitute a far closer to reality model system than monoclonal cell lines. The constant uptake into the depth of the tissue slices underlines the systems' potential for drug delivery into solid tumors.

The Low Toxicity of Graphene Quantum Dots is Reflected by Marginal Gene Expression Changes of Primary Human Hematopoietic Stem Cells

Graphene quantum dots (GQDs) are a promising next generation nanomaterial with manifold biomedical applications. For real world applications, comprehensive studies on their influence on the functionality of primary human cells are mandatory. Here, we report the effects of GQDs on the transcriptome of CD34+ hematopoietic stem cells after an incubation time of 36 hours. Of the 20 800 recorded gene expressions, only one, namely the selenoprotein W, 1, is changed by the GQDs in direct comparison to CD34+ hematopoietic stem cells cultivated without GQDs. Only a meta analysis reveals that the expression of 1171 genes is weakly affected, taking into account the more prominent changes just by the cell culture. Eight corresponding, weakly affected signaling pathways are identified, which include, but are not limited to, the triggering of apoptosis. These results suggest that GQDs with sizes in the range of a few nanometers hardly influence the CD34+ cells on the transcriptome level after 36 h of incubation, thereby demonstrating their high usability for in vivo studies, such as fluorescence labeling or delivery protocols, without strong effects on the functional status of the cells.

Nonmonotonic Classical Magnetoconductivity of a Two-Dimensional Electron Gas in a Disordered Array of Obstacles

Magnetotransport measurements in combination with molecular dynamics simulations on two-dimensional disordered Lorentz gases in the classical regime are reported. In quantitative agreement between experiment and simulation, the magnetoconductivity displays a pronounced peak as a function of the perpendicular magnetic field B which cannot be explained by existing kinetic theories. This peak is linked to the onset of a directed motion of the electrons along the contour of the disordered obstacle matrix when the cyclotron radius becomes smaller than the size of the obstacles. This directed motion leads to transient superdiffusive motion and strong scaling corrections in the vicinity of the insulator-to-conductor transitions of the Lorentz gas.

Uptake dynamics of graphene quantum dots into primary human blood cells following in vitro exposure

Human leukocytes obtained from samples of leukapheresis products of three healthy donors stimulated by granulocyte colony stimulating factor (G-CSF) were exposed to graphene quantum dots.

Antagonism between granulocytic maturation and deacetylase inhibitor-induced apoptosis in acute promyelocytic leukaemia cells

Background:

Transcriptional repression is a key mechanism driving leukaemogenesis. In acute promyelocytic leukaemia (APL), the fusion protein promyelocytic leukaemia-retinoic acid receptor-α fusion (PML-RARα) recruits transcriptional repressors to myeloid differentiation genes. All-trans-retinoic acid (ATRA) induces the proteasomal degradation of PML-RARα and granulocytic differentiation. Histone deacetylases (HDACs) fall into four classes (I–IV) and contribute to the transcription block caused by PML-RARα.

Methods:

Immunoblot, flow cytometry, and May-Grünwald–Giemsa staining were used to analyze differentiation and induction of apoptosis.

Results:

A PML-RARα- and ATRA-dependent differentiation programme induces granulocytic maturation associated with an accumulation of the myeloid transcription factor CCAAT/enhancer binding protein (C/EBP)ɛ and of the surface protein CD11b. While this process protects APL cells from inhibitors of class I HDAC activity, inhibition of all Zinc-dependent HDACs (classes I, II, and IV) with the pan-HDACi (histone deacetylase inhibitor(s)) LBH589 induces apoptosis of immature and differentiated APL cells. LBH589 can eliminate C/EBPɛ and the mitochondrial apoptosis regulator B-cell lymphoma (BCL)-xL in immature and differentiated NB4 cells. Thus, BCL-xL and C/EBPɛ are newly identified molecular markers for the efficacy of HDACi against APL cells.

Conclusions:

Our results could explain the therapeutic limitations occurring with ATRA and class I HDACi combinations. Pro-apoptotic effects caused by pan-HDAC inhibition are not blunted by ATRA-induced differentiation and may provide a clinically interesting alternative.

SIAH ubiquitin ligases target the nonreceptor tyrosine kinase ACK1 for ubiquitinylation and proteasomal degradation

Activated Cdc42-associated kinase 1 (ACK1) is a nonreceptor tyrosine kinase linked to cellular transformation. The aberrant regulation of ACK1 promotes tumor progression and metastasis. Therefore, ACK1 is regarded as a valid target in cancer therapy. Seven in absentia homolog (SIAH) ubiquitin ligases facilitate substrate ubiquitinylation that targets proteins to the proteasomal degradation pathway. Here we report that ACK1 and SIAH1 from Homo sapiens interact in a yeast two-hybrid screen. Protein-protein interaction studies and protein degradation analyses using deletion and point mutants of ACK1 verify that SIAH1 and the related SIAH2 interact with ACK1. The association between SIAHs and ACK1 depends on the integrity of a highly conserved SIAH-binding motif located in the far C-terminus of ACK1. Furthermore, we demonstrate that the interaction of ACK1 with SIAH1 and the induction of proteasomal degradation of ACK1 by SIAH1 are independent of ACK1's kinase activity. Chemical inhibitors blocking proteasomal activity corroborate that SIAH1 and SIAH2 destabilize the ACK1 protein by inducing its proteasomal turnover. This mechanism apparently differs from the lysosomal pathway targeting ACK1 after stimulation with the epidermal growth factor. Our data also show that ACK1, but not ACK1 mutants lacking the SIAH binding motif, has a discernable negative effect on SIAH levels. Additionally, knockdown approaches targeting the SIAH2 mRNA uncover specifically that the induction of SIAH2 expression, by hormonally-induced estrogen receptor (ER) activation, decreases the levels of ACK1 in luminal human breast cancer cells. Collectively, our data provide novel insights into the molecular mechanisms modulating ACK1 and they position SIAH ubiquitin ligases as negative regulators of ACK1 in transformed cells.

Impurity and edge roughness scattering in graphene nanoribbons: the Boltzmann approach

The conductivity of graphene nanoribbons in the presence of bulk impurities and edge roughness is studied theoretically using the Boltzmann transport equation for quasi-one-dimensional systems. As the number of occupied subbands increases, the conductivity due to bulk impurities converges towards the two-dimensional case. It is shown that the dependence of the conductivity generated by edge roughness scattering depends in a distinctly different way on the sample parameters than the conductivity due to bulk scattering. The Boltzmann model furthermore predicts the amplitude of the edge-roughness-induced magnetoconductance dip as a function of the amplitude and the correlation length of the edge roughness.

Quantized magnetic confinement in quantum wires

Ballistic quantum wires are exposed to longitudinal profiles of perpendicular magnetic fields composed of a spike and a homogeneous part. An asymmetric magnetoconductance peak as a function of the homogeneous magnetic field is found, comprising quantized conductance steps in the interval where the homogeneous magnetic field and the magnetic barrier have identical polarities, and a characteristic shoulder with several resonances in the interval of opposite polarities. The observations are interpreted in terms of inhomogeneous diamagnetic shifts of the quantum wire modes leading to magnetic confinement.

Histone deacetylase inhibitors and hydroxyurea modulate the cell cycle and cooperatively induce apoptosis

Therapy resistance represents a major problem for disease management in oncology. Histone deacetylase inhibitors (HDACi) have been shown to modulate the cell cycle, to induce apoptosis and to sensitize cancer cells for other chemotherapeutics. Our study shows that the HDACi valproic acid (VPA) and the ribonucleotide reductase inhibitor hydroxyurea (HU) potentiate the pro-apoptotic effects of each other towards several cancer cell lines. This correlates with the HU-induced degradation of the cyclin-dependent kinase inhibitors (CDKI) p21 and p27, mediated by the proteasome or caspase-3. Moreover, we found that caspase-3 activation is required for VPA-induced apoptosis. Remarkably, p21 and p27 can confer resistance against VPA and HU. Both CDKI interact with caspase-3 and compete with other caspase-3 substrates. Hence, p21 and p27 may contribute to chemotherapy resistance as apoptosis inhibitors. Since the biological effects of VPA and HU could be achieved at concentrations used in current treatment protocols, the combined application of these compounds might be considered as a potential strategy for cancer treatment.

Relationship between chain length, disorder, and resistivity in polypyrrole films

The effects of the polymerization temperature and of voltammetric cycling on the chain length and the resistivity of polypyrrole films are investigated. The studies provide further proof for the existence of at least two different types of polypyrrole, the so-called PPy I and PPy II. As the electropolymerization of conjugated systems in contrast to normal polymerization reactions is a fully activated process, the generation of these different types of PPy depends on experimental parameters such as temperature or formation potentials. UV-vis measurements demonstrate that PPy II comprises significantly shorter chains than PPy I (8-12 vs 32-64 units); moreover, film conductivity is found to increase with the fraction of PPy II. This fraction is changed via the polymerization temperature as well as by cyclic voltammetry, both of which can induce a metal-insulator transition. The counter-intuitive relationship between resistivity and chain length is interpreted in terms of disorder-dominated transport, in which the shorter chains of PPy II support the formation of delocalized electronic states, thereby increasing the localization length. Thus, our results are in agreement with recent broadband reflectivity measurements.

Valproic acid (VPA) in patients with refractory advanced cancer: a dose escalating phase I clinical trial

Altered histone deacetylase (HDAC) activity has been identified in several types of cancer. This study was designed to determine the safety and maximum tolerated dose (MTD) of valproic acid (VPA) as an HDAC inhibitor in cancer patients. Twenty-six pre-treated patients with progressing solid tumours were enrolled in dose-escalating three-patient cohorts, starting at a dose of VPA 30 mg kg(-1) day(-1). VPA was administered as an 1-h infusion daily for 5 consecutive days in a 21-day cycle. Neurocognitive impairment dominated the toxicity profile, with grade 3 or 4 neurological side effects occurring in 8 out of 26 patients. No grade 3 or 4 haematological toxicity was observed. The MTD of infusional VPA was 60 mg kg(-1) day(-1). Biomonitoring of peripheral blood lymphocytes demonstrated the induction of histone hyperacetylation in the majority of patients and downmodulation of HDAC2. Pharmacokinetic studies showed increased mean and maximum serum VPA concentrations >120 and >250 mg l(-1), respectively, in the 90 and 120 mg kg(-1) cohorts, correlating well with the incidence of dose-limiting toxicity (DLT). Neurotoxicity was the main DLT of infusional VPA, doses up to 60 mg kg(-1) day(-1) for 5 consecutive days are well tolerated and show detectable biological activity. Further investigations are warranted to evaluate the effectivity of VPA alone and in combination with other cytotoxic drugs.

Negative glucocorticoid receptor response elements and their role in glucocorticoid action

The glucocorticoid receptor (GR) belongs to the steroid hormone receptor subclass of nuclear receptors and controls physiological processes through activation and repression of specific target genes. The ligand-activated receptor dimer activates gene expression by binding to specific DNA sequences (glucocorticoid response element, GRE) in the promoter regions of glucocorticoid-regulated genes. In contrast to the regulation of these classical GREs, the repression of negatively regulated target genes is mediated by negative GREs (nGRE), composite GREs or by transrepression. Due to their broad therapeutic spectrum and superior therapeutic effects glucocorticoids (GCs) are the most effective drugs used for the treatment of acute and chronic inflammatory diseases. Unfortunately, long term systemic therapy with GCs is restricted due to their metabolic side effects. It is assumed that transrepression of transcription factors such as AP-1 and NF-kappa B is the main mechanism by which glucocorticoids mediate their anti-inflammatory activity, whereas the side effects of GCs are mainly mediated by GR-DNA-interaction either by activation or by negative regulation of gene expression. While trans-repression has been characterized in detail, the molecular mechanisms of DNA-dependent cis-repression remain unclear. In this review, we focus on current knowledge about nGRE-mediated target gene repression and the relevance and function of these genes for glucocorticoid action. Negative GREs contribute to the regulation of the hypothalamic-pituitary-adrenal (HPA) axis (POMC and CRH), bone (osteocalcin) and skin (keratins) function, inflammation (IL-1beta), angiogenesis (proliferin) and lactation (prolactin). The discovery of the underlying mechanisms, especially the comparison to positive GREs and trans-repression may help in the future to discover and analyze novel selective GR agonists.

Energy spectra of quantum rings

Quantum mechanical experiments in ring geometries have long fascinated physicists. Open rings connected to leads, for example, allow the observation of the Aharonov-Bohm effect, one of the best examples of quantum mechanical phase coherence. The phase coherence of electrons travelling through a quantum dot embedded in one arm of an open ring has also been demonstrated. The energy spectra of closed rings have only recently been studied by optical spectroscopy. The prediction that they allow persistent current has been explored in various experiments. Here we report magnetotransport experiments on closed rings in the Coulomb blockade regime. Our experiments show that a microscopic understanding of energy levels, so far limited to few-electron quantum dots, can be extended to a many-electron system. A semiclassical interpretation of our results indicates that electron motion in the rings is governed by regular rather than chaotic motion, an unexplored regime in many-electron quantum dots. This opens a way to experiments where even more complex structures can be investigated at a quantum mechanical level.

Histone deacetylase as a therapeutic target

The maintenance of health depends on the coordinated and tightly regulated expression of genetic information. Certain forms of leukemia have become paradigms for the pathogenic role of aberrant repression of differentiation genes. In these acute leukemias, fusion proteins generated by chromosomal translocations no longer function as transcriptional activators, but instead repress target genes by recruiting histone deacetylases (HDACs). The potential benefit of HDAC inhibition has been established by the use of enzyme inhibitors in vitro and in a single reported case of experimental therapy. Because recently identified HDAC inhibitors appear to overcome many drawbacks of early inhibitory compounds in clinical use, the stage is set to test the therapeutic value of HDAC inhibition in leukemias and in other diseases, including solid tumors and aberrant hormonal signaling. This review summarizes the range of diseases expected to respond to HDAC inhibition.

Multiple regions of ETO cooperate in transcriptional repression

In acute myeloid leukemias (AMLs) with t(8;21), the transcription factor AML1 is juxtaposed to the zinc finger nuclear protein ETO (Eight-Twenty-One), resulting in transcriptional repression of AML1 target genes. ETO has been shown to interact with corepressors, such as N-CoR and mSin3A to form complexes containing histone deacetylases. To define regions of ETO required for maximal repressor activity, we analyzed amino-terminal deletions in a transcriptional repression assay. We found that ETO mutants lacking the first 236 amino acids were not affected in their repressor activity, whereas a further deletion of 85 amino acids drastically reduced repressor function and high molecular weight complex formation. This latter mutant can still homodimerize and bind to N-CoR but shows only weak binding to mSin3A. Furthermore, we could show that a "core repressor domain" comprising nervy homology region 2 and its amino- and carboxyl-terminal flanking sequences recruits mSin3A and induces transcriptional repression. These results suggest that mSin3A and N-CoR bind to ETO independently and that both binding sites cooperate to maximize ETO-mediated transcriptional repression. Thus, ETO has a modular structure, and the interaction between the individual elements is essential for the formation of a stable repressor complex and efficient transcriptional repression.

Shot noise by quantum scattering in chaotic cavities

We have experimentally studied shot noise of chaotic cavities defined by two quantum point contacts in series. The cavity noise is determined as (1/4)2e/I/ in agreement with theory and can be well distinguished from other contributions to noise generated at the contacts. Subsequently, we have found that cavity noise decreases if one of the contacts is further opened and reaches nearly zero for a highly asymmetric cavity. Heating inside the cavity due to electron-electron interaction can slightly enhance the noise of large cavities and is also discussed quantitatively.

Signatures of spin pairing in chaotic quantum dots

Coulomb blockade resonances are measured in a GaAs quantum dot in which both shape deformations and interactions are small. The parametric evolution of the Coulomb blockade peaks shows a pronounced pair correlation in both position and amplitude, which is interpreted as spin pairing. As a consequence, the nearest-neighbor distribution of peak spacings can be well approximated by a modified bimodal Wigner surmise, in which interactions are taken into account beyond the constant interaction model.

Analysis of the metallic phase of two-dimensional holes in SiGe in terms of temperature dependent screening

We find that temperature dependent screening can quantitatively explain the metallic behavior of the resistivity on the metallic side of the so-called metal-insulator transition in p-SiGe. Interference and interaction effects exhibit the usual insulating behavior which is expected to overpower the metallic background at sufficiently low temperatures. We find empirically that the concept of a Fermi liquid describes our system with its large interaction parameter r(s) approximately 8.

VDR-Alien: a novel, DNA-selective vitamin D(3) receptor-corepressor partnership

The vitamin D receptor (VDR) is a transcription factor that transmits incoming 1,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2)D(3)) signaling via combined contact with coactivator proteins and specific DNA binding sites (VDREs), which ultimately results in activation of transcription. In contrast, the mechanisms of transcriptional repression via the VDR are less well understood. This study documents VDR-dependent transcriptional repression largely via histone deacetylase (HDAC) activity. Direct, ligand-sensitive protein-protein interaction of the VDR with the nuclear receptor corepressor (NCoR) and a novel corepressor, called Alien, was demonstrated to be comparable but independent of the VDR AF-2 trans-activation domain. Functional assays indicated that Alien, but not NCoR, displays selectivity for different VDRE structures for transferring these repressive effects into gene regulatory activities. Moreover, superrepression via Alien was found to be affected only in part by HDAC inhibitors such as trichostatin A. Finally, for a dissociation of VDR-Alien complexes in vitro and in vivo, higher ligand concentrations were needed than for a dissociation of VDR-NCoR complexes. This suggests that Alien and NCoR are using different interfaces for interaction with the VDR and different pathways for mediating superrepression, which in turn characterizes Alien as a representative of a new class of corepressors. Taken together, association of the VDR with corepressor proteins provides a further level of transcriptional regulation, which is emerging as a complex network of protein-protein interaction-mediated control.

The fermionic hanbury brown and twiss experiment

A Hanbury Brown and Twiss experiment for a beam of electrons has been realized in a two-dimensional electron gas in the quantum Hall regime. A metallic split gate serves as a tunable beam splitter to partition the incident beam into transmitted and reflected partial beams. In the nonequilibrium case the fluctuations in the partial beams are shown to be fully anticorrelated, demonstrating that fermions exclude each other. In equilibrium, the cross-correlation of current fluctuations at two different contacts is also found to be negative and nonzero, provided that a direct transmission exists between the contacts.

Signal-specific co-activator domain requirements for Pit-1 activation

POU-domain proteins, such as the pituitary-specific factor Pit-1, are members of the homeodomain family of proteins which are important in development and homeostasis, acting constitutively or in response to signal-transduction pathways to either repress or activate the expression of specific genes. Here we show that whereas homeodomain-containing repressors such as Rpx2 seem to recruit only a co-repressor complex, the activity of Pit-1 is determined by a regulated balance between a co-repressor complex that contains N-CoR/SMRT, mSin3A/B and histone deacetylases, and a co-activator complex that includes the CREB-binding protein (CBP) and p/CAF. Activation of Pit-1 by cyclic AMP or growth factors depends on distinct amino- and carboxy-terminal domains of CBP, respectively. Furthermore, the histone acetyltransferase functions of CBP or p/CAF are required for Pit-1 function that is stimulated by cyclic AMP or growth factors, respectively. These data show that there is a switch in specific requirements for histone acetyltransferases and CBP domains in mediating the effects of different signal-transduction pathways on specific DNA-bound transcription factors.

Diverse signaling pathways modulate nuclear receptor recruitment of N-CoR and SMRT complexes

Several lines of evidence indicate that the nuclear receptor corepressor (N-CoR) complex imposes ligand dependence on transcriptional activation by the retinoic acid receptor and mediates the inhibitory effects of estrogen receptor antagonists, such as tamoxifen, suppressing a constitutive N-terminal, Creb-binding protein/coactivator complex-dependent activation domain. Functional interactions between specific receptors and N-CoR or SMRT corepressor complexes are regulated, positively or negatively, by diverse signal transduction pathways. Decreased levels of N-CoR correlate with the acquisition of tamoxifen resistance in a mouse model system for human breast cancer. Our data suggest that N-CoR- and SMRT-containing complexes act as rate-limiting components in the actions of specific nuclear receptors, and that their actions are regulated by multiple signal transduction pathways.

Differential effects of nuclear receptor corepressor (N-CoR) expression levels on retinoic acid receptor-mediated repression support the existence of dynamically regulated corepressor complexes

Thyroid hormone and retinoic acid receptors are members of the nuclear receptor superfamily of ligand-dependent transcription factors that stimulate the transcription of target genes in the presence of activating ligands and repress transcription in their absence. Transcriptional repression by the thyroid hormone and retinoic acid receptors has been proposed to be mediated by the nuclear receptor corepressor, N-CoR, or the related factor, SMRT (silencing mediator of retinoic acid and thyroid hormone receptors). Recent studies have suggested that transcriptional repression by N-CoR involves a corepressor complex that also contains mSin3A/B and the histone deacetylase, RPD3. In this manuscript, we demonstrate that transcriptional repression by the retinoic acid receptor can be either positively or negatively regulated by changes in the levels of N-CoR expression, suggesting a relatively strict stoichiometric relationship between N-CoR and other components of the corepressor complex. Consistent with this interpretation, overexpression of several functionally defined domains of N-CoR also relieve repression by nuclear receptors. N-CoR is distributed throughout the nucleus in a nonuniform pattern, and a subpopulation becomes concentrated into several discrete dot structures when highly expressed. RPD3 is also widely distributed throughout the nucleus in a nonuniform pattern. Simultaneous imaging of RPD3 and N-CoR suggest that a subset of each of these proteins colocalize, consistent with the existence of coactivator complexes containing both proteins. In addition, a substantial fraction of both N-CoR and mSin3 A/B appear to be independently distributed. These observations suggest that interactions between RPD3 and Sin3/N-CoR complexes may be dynamically regulated.

A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression

Transcriptional repression by nuclear receptors has been correlated to binding of the putative co-repressor, N-CoR. A complex has been identified that contains N-CoR, the Mad presumptive co-repressor mSin3, and the histone deacetylase mRPD3, and which is required for both nuclear receptor- and Mad-dependent repression, but not for repression by transcription factors of the ets-domain family. These data predict that the ligand-induced switch of heterodimeric nuclear receptors from repressor to activator functions involves the exchange of complexes containing histone deacetylases with those that have histone acetylase activity.

A CBP integrator complex mediates transcriptional activation and AP-1 inhibition by nuclear receptors

Nuclear receptors regulate gene expression by direct activation of target genes and inhibition of AP-1. Here we report that, unexpectedly, activation by nuclear receptors requires the actions of CREB-binding protein (CBP) and that inhibition of AP-1 activity is the apparent result of competition for limiting amounts of CBP/p300 in cells. Utilizing distinct domains, CBP directly interacts with the ligand-binding domain of multiple nuclear receptors and with the p160 nuclear receptor coactivators, which upon cloning have proven to be variants of the SRC-1 protein. Because CBP represents a common factor, required in addition to distinct coactivators for function of nuclear receptors, CREB, and AP-1, we suggest that CBP/p300 serves as an integrator of multiple signal transduction pathways within the nucleus.

Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor

Thyroid-hormone and retinoic-acid receptors exert their regulatory functions by acting as both activators and repressors of gene expression. A nuclear receptor co-repressor (N-CoR) of relative molecular mass 270K has been identified which mediates ligand-independent inhibition of gene transcription by these receptors, suggesting that the molecular mechanisms of repression by thyroid-hormone and retinoic-acid receptors are analogous to the co-repressor-dependent transcriptional inhibitory mechanisms of yeast and Drosophila.

P-Lim, a LIM homeodomain factor, is expressed during pituitary organ and cell commitment and synergizes with Pit-1

A pituitary LIM homeodomain factor, P-Lim, is expressed as Rathke's pouch forms and as specific pituitary cell phenotypes are established, suggesting functional roles throughout pituitary development. While selectively expressed in both anterior and intermediate pituitary in mature mice, P-Lim is also transiently expressed in the developing ventral neural cord and brainstem. P-Lim binds to and activates the promoter of the alpha-glycoprotein subunit gene, a marker of early pituitary development, and synergizes with Pit-1 in transcriptional activation of genes encoding terminal differentiation markers. The LIM domain of P-Lim specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.

C1 repressor-mediated DNA looping is involved in C1 autoregulation of bacteriophage P1

C1 repressor is required to repress the lytic functions of a P1 prophage in vivo. Transcription of the c1 gene is autoregulated via the C1-controlled operator Op99a,b which overlaps the promoter of the c1 gene. It is negatively affected by Lxc corepressor and the DNA region upstream of c1, which contains the additional operators Op99c, d, and e. We have explored these effects by constructing a set of lacZ reporter plasmids with Op99a,b and varying parts of the upstream DNA region. Transcription levels were measured in vivo with a two-plasmid system containing the lacZ reporter and a c1+ lxc+ or c1+ lxc- plasmid. Compared to the C1+Lxc-repressed lacZ reporter with all operators present, the basal level of beta-galactosidase activity increases successively when (i) upstream operators were deleted or inactivated, (ii) Lxc corepressor was removed, and (iii) C1 and Lxc were absent. By that means a 2 x 2 x 15-fold stepwise increase in enzyme activity was found. Using electron microscopy to visualize the interaction of C1 repressor with the operators in vitro, looped DNA molecules were observed. Although all operators can participate in C1-mediated DNA looping, loops between Op99a,b and Op99d occurred predominantly. Lxc is not required but increases drastically the frequency of loop formation. The results indicate that C1-mediated DNA looping may be a second element besides Lxc for fine-tuning the autoregulation of c1 transcription.

The Bof protein of bacteriophage P1 exerts its modulating function by formation of a ternary complex with operator DNA and C1 repressor

Bacteriophage P1 encodes several regulatory elements for the lytic or lysogenic response, which are located in the immC, immI, and immT regions. Their products are the C1 repressor of lytic functions with the C1 inactivator protein Coi, the C4 repressor of antirepressor synthesis and the modulator protein Bof, respectively. We have studied in vitro the interaction of the components of the immC and immT regions with C1-controlled operators using highly purified Bof, C1, and Coi proteins. Bof protein (M(r) = 9,800) does not interact with C1 repressor alone, but as shown by DNA mobility shift experiments, in the presence of C1 repressor Bof binds to all operators tested by forming a C1.Bof-operator DNA ternary complex. The effect of this complex formation was studied in more detail with the operator of the c1 gene. Here, Bof only marginally alters the C1 repressor footprint at Op99a,b, but nevertheless considerably influences the repressibility of the operator.promoter element: (i) the autoregulated c1 mRNA synthesis is further down-regulated and (ii) the ability of Coi protein to dissociate the C1.operator DNA complex is strongly inhibited. We suggest that Bof protein functions by modulating C1 repression of many widely dispersed operators on the prophage genome.

C1 repressor of phage P1 is inactivated by noncovalent binding of P1 Coi protein

The temperate phage P1 encodes two genes whose products antagonize the action of the phage's C1 repressor of lytic functions, namely a distantly linked antirepressor gene, ant, and a closely linked c1 inactivator gene, coi. Starting with an inducible coi-recombinant plasmid, Coi protein was overproduced and purified to near homogeneity. By using a DNA mobility shift assay we demonstrate that Coi protein inhibits the operator binding of the C1 repressors of the closely related P1 and P7 phages. Coi protein (Mr = 7,600) exerts its C1-inactivating function by forming a complex with the C1 repressor (Mr = 32,500) at a molar ratio of about 1:1, as shown by density gradient centrifugation and gel filtration. C1 repressor and Coi protein are recovered in active form from the complex, suggesting that noncovalent interactions are the sole requirements for complex formation. The interplay of repressor and antagonists operating in the life cycle of P1 is discussed.

The c1 repressor inactivator protein coi of bacteriophage P1. Cloning and expression of coi and its interference with c1 repressor function

The immC region of bacteriophage P1 contains the c1 repressor gene and its upstream region with four c1-controlled operators and four open reading frames. A c1 inactivator gene, coi, was defined by mutations in immC that suppress the virulence of the P1virC mutation. The exact location of the coi gene was not known (Scott, J.R. (1980) Curr. Top. Microbiol. Immunol. 90, 49-65). When a variety of P1 immC fragments were inserted into an expression vector, a gene product was inducible for the open reading frame 4 only. We identify this product as the c1 inactivator protein, coi by the following criteria: (a) expression of coi from a recombinant plasmid induces the P1 prophage and inhibits lysogenization of sensitive bacteria by P1; (b) all c1-controlled operator-promoter elements tested in vivo are derepressed by coi; (c) a partially purified coi protein (apparent molecular weight = 4800) interacts with c1 repressor and inhibits its binding to the operator in vitro. Based on these results we refine a model for the regulation of those genes and elements within immC which participate in the decision of P1 to enter the lytic or lysogenic pathway.

ban operon of bacteriophage P1. Mutational analysis of the c1 repressor-controlled operator

The repressor of bacteriophage P1, encoded by the c1 gene, represses the phage lytic functions and is responsible for maintaining the P1 prophage in the lysogenic state. The c1 repressor interacts with at least 11 binding sites or operators widely scattered over the P1 genome. From these operators, a 17 base-pair asymmetric consensus sequence, ATTGCTCTAATAAATTT, was derived. Here, we show that the operator, Op72 of the P1ban operon consists of two overlapping 17 base-pair sequences a and b forming an incomplete palindrome. Op72a matches the consensus sequence, whereas Op72b contains two mismatches. The evidence is based on the sequence analysis of 27 operator mutants constitutive for ban expression. They were identified as single-base substitutions at positions 2 to 10 of Op72a (26 mutants) and at position 8 of Op72b (one mutant). We conclude from gel retardation and footprinting studies that two repressor molecules bind to the operator and that positions 4, 5 and 7 to 10 of the operator play an essential role in repressor recognition.