Novel Mechanism Of Transcriptional Regulation Research Articles

Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens.

Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.

Transcriptomic profiling identifies novel mechanisms of transcriptional regulation of the cytochrome P450 (Cyp)3a11 gene

Cytochrome P450 (CYP)3A is the most abundant CYP enzyme in the human liver, and a functional impairment of this enzyme leads to unanticipated adverse reactions and therapeutic failures; these reactions result in the early termination of drug development or the withdrawal of drugs from the market. The transcriptional regulation mechanism of the Cyp3a gene is not fully understood and requires a thorough investigation. We mapped the transcriptome of the Cyp3a gene in a mouse model. The Cyp3a gene was induced using the mPXR activator pregnenolone-16alpha-carbonitrile (PCN) and was subsequently downregulated using lipopolysaccharide (LPS). Our objective was to identify the transcription factors (TFs), epigenetic modulators and molecular pathways that are enriched or repressed by PCN and LPS based on a gene set enrichment analysis. Our analysis shows that 113 genes were significantly upregulated (by at least 1.5-fold) with PCN treatment, and that 834 genes were significantly downregulated (by at least 1.5-fold) with LPS treatment. Additionally, the targets of the 536 transcription factors were enriched by a combined treatment of PCN and LPS, and among these, 285 were found to have binding sites on Cyp3a11. Moreover, the repressed targets of the epigenetic markers HDAC1, HDAC3 and EZH2 were further suppressed by LPS treatment and were enhanced by PCN treatment. By identifying and contrasting the transcriptional regulators that are altered by PCN and LPS, our study provides novel insights into the transcriptional regulation of CYP3A in the liver.

Novel mechanisms of transcriptional regulation of vitamin and co‐factor metabolism in Archaea

Water-soluble B-type vitamins are essential components of the cellular metabolism in all three kingdoms of life. In contrast to Bacteria, little is known about the metabolic pathways of vitamin biosynthesis and salvage in Archaea. Bacteria utilize several types of vitamin-responsive RNA riboswitches and transcriptional factors to control expression of their vitamin biosynthesis and transport genes, however no such regulatory mechanisms were found in Archaea. We used the comparative genomics approach to identify genes involved in the biosynthesis and salvage of four B-type vitamins (B1, B2, B3 and B12) in complete genomes of Archaea. For each vitamin metabolic pathway, we identified unique DNA motifs and reconstructed the putative regulons sharing the conserved DNA sites in diverse archaeal lineages including Sulfolobales, Thermoproteales, Desulfurococcales, Archaeoglobales, Thermoplasmatales, Thermococcales, Halobacteriales, Methanomicrobia and Thaumarchaeota. Candidate transcription factors for direct control of the identified novel regulons were identified by genome context analysis. Three novel transcriptional regulators, RbkR, ThiR and NdkR, were predicted to control the riboflavin, thiamine and NAD/niacin biosynthesis and transport genes, respectively. ThiR regulators are composed of a DNA-binding helix-turn-helix (HTH) domain and a ThiN-like domain that is similar to archaeal thiamin phosphate synthase. NdkR regulators also contains two domains, a NAD kinase domain and a DNA-binding domain, however the kinase domain in NdkR proteins is degenerated. RbkR proteins represent a fusion of a DNA-binding HTH domain and a catalytic domain that is orthologous to CTP-dependent riboflavin kinase from Methanocaldococcus jannaschii. The identified DNA binding motifs of novel regulators were experimentally validated by in vitro DNA-binding assays with the purified recombinant transcription factors RbkR and ThiR from several archaeal species. The CTP-dependent riboflavin kinase activity of bifunctional RbkR proteins was confirmed by in vitro enzymatic assay. We have solved the crystal structures of the apo and DNA operator-bound forms of RbkR from Thermoplasma acidophilum and compared them with the previously determined structure of riboflavin kinase from M. jannaschii. The majority of CDP- and FMN-binding residues in the kinase protein are well conserved in RbkR proteins. In the structure of the RbkR-DNA dimeric complex, we found residues involved in specific recognition of a palindromic DNA site. However, both the candidate RbkR-binding DNA motifs and contacting residues in HTH domains showed significant variability between archaeal lineages. Further experimental investigations of divergent RbkR memners are required to achieve a better understanding of their DNA-specificity determinants. In summary, we have identified novel regulators for transcriptional control of vitamin metabolism genes in Archaea. The reconstructed regulons contains novel candidate vitamin uptake transporters. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in Archaea. Support or Funding Information This research was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), and U.S. Department of Energy (DOE) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area. Figure 1Open in figure viewerPowerPoint Transcriptional regulation of riboflavin metabolism genes by a novel bifunctional repressor/kinase protein in Pyrobaculum yellowstonensis.

Abstract A29: Hypoxia regulated long noncoding RNAs and antisense transcripts in breast cancer: Novel insights of noncoding transcriptional regulation in hypoxic microenvironment

Abstract Tumour hypoxia is a common feature of tumour microenvironment and contributes to an aggressive phenotype across multiple types of cancers. Hypoxia-inducible factor (HIF) is a key element regulating expression of hundreds of coding and non-coding RNAs, which act to both improve oxygen delivery and to reduce cellular demand of oxygen. We performed a comprehensive analysis on hypoxic transcription landscape and epigenetic markers of transcriptional activation in MCF-7 breast cancer cells under hypoxia using next generation sequencing. Analyses revealed that all classes of non-coding RNA are profoundly regulated by hypoxia including piwiRNA, miRNA, tRNA, and sn/snoRNA. Analysis revealed downregulation of snRNAs and tRNAs in hypoxia, whereas miRNAs, antisense transcripts and lncRNAs are globally upregulated in hypoxia. Many novel natural antisense transcripts are induced under hypoxia and their expression is dependent on HIF. Hypoxia-induced natural antisense transcripts are associated with both induction and repression in cis. Moreover, large numbers of lncRNAs are found overexpressed under hypoxia and are associated with HIF binding and elevated level of RNApol2 and H3K4me3, suggesting direct transcriptional regulation of lncRNAs by HIF. Among the most hypoxia induced lncRNA was NEAT1, which is a direct transcriptional target of HIF-2α. We confirmed the hypoxic NEAT1 upregulation in a number of breast cancer cell lines and in tumour xenografts models treated with bevacizumab. Hypoxia induced NEAT1 directly increase the formation of nuclear paraspeckles bodies. Moreover, hypoxic induction of NEAT1 contributes to increase cell proliferation, cell survival, and inhibit apoptosis. Furthermore, we found that NEAT1 is required to retain hypoxia induced hyper edited Junctional Adhesion Molecule A (JAM-A) mRNA in nucleus to inhibit its translation. Finally, in a large breast cancers cohort, high expression of NEAT1 is linked with poor prognosis and with different clinicopathological features. Our results extend knowledge of the hypoxic transcriptional response into the spectrum of non-coding transcripts. These findings provide novel mechanisms of transcriptional regulation in hypoxic tumours through non-coding RNAs and open new avenues to find novel pathways and targets to develop therapies for breast cancer. Citation Format: Hani Choudhry, Ashwag Albukhari, Matteo Morotti, Syed Haider, Daniela Moralli, Johannes Schödel, Catherine Green, Carme Camps, Francesca Buffa, Peter Ratcliffe, Ioannis Ragoussis, David Mole, Adrian Harris. Hypoxia regulated long noncoding RNAs and antisense transcripts in breast cancer: Novel insights of noncoding transcriptional regulation in hypoxic microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A29.

Abstract P2-05-01: The non-coding transcriptome of hypoxic breast cancer: Novel insights of clinical relevant long non-coding RNA in hypoxia signalling

Abstract Hypoxia is associated with aggressive and poor prognosis of breast cancer. Generally, pan-genome analyses of hypoxia have focussed on protein-coding genes, however, the role of non-coding RNAs, in particular long non-coding RNAs (lncRNA) in hypoxia is not well characterised. We undertook an integrated genomic analysis of the hypoxic transcriptome in MCF7 breast cancer cells, employing total RNA-seq together with ChIP-seq for the hypoxia-inducible transcription factor (HIF) and for epigenetic marks of transcriptional activation (RNApol2 and histone H3K4me3). Analyses revealed that all classes of RNA are significantly regulated by hypoxia including piwiRNA, miRNA, tRNA, and sn/snoRNA. Significant numbers of lncRNAs were upregulated in hypoxia and were associated with increased RNApol2 and H3K4me3 markers and with HIF binding, indicating direct transcriptional activation of lncRNAs by HIF. The most hypoxiclly upregulated lncRNA was NEAT1, which is a direct transcriptional target of HIF-2a but not HIF-1a. The role of NEAT1 in cancer has not been previously studied. We demonstrated that hypoxic NEAT1 induction is common in breast cancer cell lines and xenografts models treated with bevacizumab. NEAT1 directly induces the formation of nuclear paraspeckle bodies in hypoxia. Moreover, it contributes to tumourigenicity by increasing cell proliferation, colony formation, and reducing apoptosis. In addition, we report that NEAT1 is required to retain hypoxia induced hyper edited Junctional Adhesion Molecule A (JAM-A) mRNA in the nucleus, thus preventing export into the cytoplasm for translation. Finally, in a large cohort of 2000 breast cancers, high levels of NEAT1 were associated with poor clinical outcomes and clinicopathological features. Our results extend knowledge of the hypoxic transcriptional response into the spectrum of non-coding transcripts. These findings provide novel mechanisms of transcriptional regulation in hypoxia and open new avenues to find novel pathways and targets to develop therapies for breast cancer. Citation Format: Hani Choudhry, Johannes Schodel, Ashwag Albukhari, Syed Haider, Francesca Buffa, Peter J Ratcliffe, David R Mole, Ioannis Ragousis, Adrian L Harris. The non-coding transcriptome of hypoxic breast cancer: Novel insights of clinical relevant long non-coding RNA in hypoxia signalling [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-01.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum

Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family.

Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon

Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical ~20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluorescent protein (GFP) stop codon, GFP expression was similarly reduced. Rap1p mediated this down-regulation, as shown by mutagenesis and chromatin immunoprecipitation. A regular threefold drop is observed in different contexts, suggesting utility for synthetic circuits. A large reduction of RNAP II occupancy on the CO-Ty1 construct was observed 3' to the identified Rap1p site and a novel 3' truncated RNA species was observed. We propose a novel mechanism of transcriptional regulation by Rap1p whereby it serves as a transcriptional roadblock when bound to transcription unit sequences.

Identification of Transcription Factor E3 (TFE3) as a Receptor-independent Activator of Gα16: GENE REGULATION BY NUCLEAR Gα SUBUNIT AND ITS ACTIVATOR

Receptor-independent G-protein regulators provide diverse mechanisms for signal input to G-protein-based signaling systems, revealing unexpected functional roles for G-proteins. As part of a broader effort to identify disease-specific regulators for heterotrimeric G-proteins, we screened for such proteins in cardiac hypertrophy using a yeast-based functional screen of mammalian cDNAs as a discovery platform. We report the identification of three transcription factors belonging to the same family, transcription factor E3 (TFE3), microphthalmia-associated transcription factor, and transcription factor EB, as novel receptor-independent activators of G-protein signaling selective for Gα(16). TFE3 and Gα(16) were both up-regulated in cardiac hypertrophy initiated by transverse aortic constriction. In protein interaction studies in vitro, TFE3 formed a complex with Gα(16) but not with Gα(i3) or Gα(s). Although increased expression of TFE3 in heterologous systems had no influence on receptor-mediated Gα(16) signaling at the plasma membrane, TFE3 actually translocated Gα(16) to the nucleus, leading to the induction of claudin 14 expression, a key component of membrane structure in cardiomyocytes. The induction of claudin 14 was dependent on both the accumulation and activation of Gα(16) by TFE3 in the nucleus. These findings indicate that TFE3 and Gα(16) are up-regulated under pathologic conditions and are involved in a novel mechanism of transcriptional regulation via the relocalization and activation of Gα(16).

Epidermal growth factor upregulates serotonin transporter in human intestinal epithelial cells via transcriptional mechanisms

Serotonin transporter (SERT) regulates extracellular availability of serotonin and is a potential pharmacological target for gastrointestinal disorders. A decrease in SERT has been implicated in intestinal inflammatory and diarrheal disorders. However, little is known regarding regulation of SERT in the intestine. Epidermal growth factor (EGF) is known to influence intestinal electrolyte and nutrient transport processes and has protective effects on intestinal mucosa. Whether EGF regulates SERT in the human intestine is not known. The present studies examined the regulation of SERT by EGF, utilizing Caco-2 cells grown on Transwell inserts as an in vitro model. Treatment with EGF from the basolateral side (10 ng/ml, 24 h) significantly stimulated SERT activity (∼2-fold, P < 0.01) and mRNA levels compared with control. EGF increased the activities of the two alternate promoter constructs for human SERT gene: SERT promoter 1 (hSERTp1, upstream of exon 1a) and SERT promoter 2 (hSERTp2, upstream of exon 2). Inhibition of EGF receptor (EGFR) tyrosine kinase activity by PD168393 (1 nM) blocked the stimulatory effects of EGF on SERT promoters. Progressive deletions of the SERT promoter indicated that the putative EGF-responsive elements are present in the -672/-472 region of the hSERTp1 and regions spanning -1195/-738 and -152/+123 of hSERTp2. EGF markedly increased the binding of Caco-2 nuclear proteins to the potential AP-1 cis-elements present in EGF-responsive regions of hSERTp1 and p2. Overexpression of c-jun but not c-fos specifically transactivated hSERTp2, with no effects on hSERTp1. Our findings define novel mechanisms of transcriptional regulation of SERT by EGF via EGFR at the promoter level that may contribute to the beneficial effects of EGF in gut disorders.

Membrane Topology and DNA-Binding Ability of the Streptococcal CpsA Protein

Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection. The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown. Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR_cpsA_psr protein family are predicted to have a single transmembrane domain. This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation. Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta-galactosidase or alkaline phosphatase. Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct. To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full-length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter. Assays revealed that full-length, purified CpsA protein binds specifically to DNA containing the capsule promoter region. Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter. This is the first demonstration of a member of this protein family interacting with its target DNA. Taken together, CpsA, as well as other members of the LytR_cpsA_psr protein family, appears to utilize a unique mechanism of transcriptional regulation.

CpG-B oligodeoxynucleotides inhibit Toll-like receptor-dependent and -independent induction of type I IFN in dendritic cells (136.10)

Abstract CpG oligodeoxynucleotides (ODNs) signal through TLR9 to induce type-I IFN (IFNαβ) in dendritic cells. CpG-A ODNs are more efficacious than CpG-B ODNs for induction of IFNαβ. Because IFNαβ may contribute to autoimmunity, it is important to identify mechanisms to inhibit induction of IFNαβ. In our studies, CpG-B ODN inhibited induction of IFNαβ by CpG-A ODN, while induction of TNFα and IL-12p40 by CpG-A ODN was not affected. CpG-B inhibition of IFNαβ was observed in Flt3L-induced murine DCs, purified murine mDCs and pDCs, and human PBMCs. CpG-B ODN inhibited induction of IFNαβ by agonists of multiple receptors, including MyD88-dependent TLRs and MyD88-independent receptors. CpG-B ODN did not inhibit the IFNαβ positive feedback loop “second wave” IFNαβ, since IFNαβ-induced expression of IFNαβ mRNA was unaffected, and CpG-B inhibition of IFNαβ was manifested in IFNαβR-/- DCs, which lack the positive feedback mechanism. Rather, CpG-B ODN inhibited early “first-wave” IFNα4 and IFNβ. Chromatin immunoprecipitation revealed that association of IRF1 with the IFNα4 and IFNβ promoters was induced by CpG-A ODN but not CpG-B ODN. Moreover, CpG-A-induced association of IRF1 with these promoters was inhibited by CpG-B ODN. Our studies demonstrate a novel mechanism of transcriptional regulation of first-wave IFNαβ that selectively inhibits induction of IFNαβ downstream of multiple receptors and may provide targets for future therapeutic inhibition of IFNαβ expression in vivo.

CpG-B Oligodeoxynucleotides Inhibit TLR-Dependent and -Independent Induction of Type I IFN in Dendritic Cells

CpG oligodeoxynucleotides (ODNs) signal through TLR9 to induce type I IFN (IFN-alphabeta) in dendritic cells (DCs). CpG-A ODNs are more efficacious than CpG-B ODNs for induction of IFN-alphabeta. Because IFN-alphabeta may contribute to autoimmunity, it is important to identify mechanisms to inhibit induction of IFN-alphabeta. In our studies, CpG-B ODN inhibited induction of IFN-alphabeta by CpG-A ODN, whereas induction of TNF-alpha and IL-12p40 by CpG-A ODN was not affected. CpG-B inhibition of IFN-alphabeta was observed in FLT3 ligand-induced murine DCs, purified murine myeloid DCs, plasmacytoid DCs, and human PBMCs. CpG-B ODN inhibited induction of IFN-alphabeta by agonists of multiple receptors, including MyD88-dependent TLRs (CpG-A ODN signaling via TLR9, or R837 or Sendai virus signaling via TLR7) and MyD88-independent receptors (polyinosinic:polycytidylic acid signaling via TLR3 or ds break-DNA signaling via a cytosolic pathway). CpG-B ODN did not inhibit the IFN-alphabeta positive feedback loop second-wave IFN-alphabeta, because IFN-alphabeta-induced expression of IFN-alphabeta was unaffected, and CpG-B inhibition of IFN-alphabeta was manifested in IFN-alphabetaR(-/-) DCs, which lack the positive feedback mechanism. Rather, CpG-B ODN inhibited early TLR-induced first wave IFN-alpha4 and IFN-beta. Chromatin immunoprecipitation revealed that association of IFN regulatory factor 1 with the IFN-alpha4 and IFN-beta promoters was induced by CpG-A ODN but not CpG-B ODN. Moreover, CpG-A-induced association of IFN regulatory factor 1 with these promoters was inhibited by CpG-B ODN. Our studies demonstrate a novel mechanism of transcriptional regulation of first-wave IFN-alphabeta that selectively inhibits induction of IFN-alphabeta downstream of multiple receptors and may provide targets for future therapeutic inhibition of IFN-alphabeta expression in vivo.

NFκB p50-CCAAT/Enhancer-binding Protein β (C/EBPβ)-mediated Transcriptional Repression of MicroRNA let-7i following Microbial Infection

MicroRNAs, central players of numerous cellular processes, regulate mRNA stability or translational efficiency. Although these molecular events are established, the mechanisms regulating microRNA function and expression remain largely unknown. The microRNA let-7i regulates Toll-like receptor 4 expression. Here, we identify a novel transcriptional mechanism induced by the protozoan parasite Cryptosporidium parvum and Gram(-) bacteria-derived lipopolysaccharide (LPS) mediating let-7i promoter silencing in human biliary epithelial cells (cholangiocytes). Using cultured cholangiocytes, we show that microbial stimulus decreased let-7i expression, and promoter activity. Analysis of the mechanism revealed that microbial infection promotes the formation of a NFkappaB p50-C/EBPbeta silencer complex in the regulatory sequence. Chromatin immunoprecipitation assays (ChIP) demonstrated that the repressor complex binds to the let-7i promoter following microbial stimulus and promotes histone-H3 deacetylation. Our results provide a novel mechanism of transcriptional regulation of cholangiocyte let-7i expression following microbial insult, a process with potential implications for epithelial innate immune responses in general.

Induction of the small heat shock protein αB-crystallin by genotoxic stress is mediated by p53 and p73

The small heat shock protein alphaB-crystallin is a molecular chaperone that is induced by stress and protects cells by inhibiting protein aggregation and apoptosis. To identify novel transcriptional regulators of the alphaB-crystallin gene, we examined the alphaB-crystallin promoter for conserved transcription factor DNA-binding elements and identified a putative response element for the p53 tumor suppressor protein. Ectopic expression of wild-type p53 induced alphaB-crystallin mRNA and protein with delayed kinetics compared to p21. Additionally, the induction of alphaB-crystallin by genotoxic stress was inhibited by siRNAs targeting p53. Although the p53-dependent transactivation of an alphaB-crystallin promoter luciferase reporter required the putative p53RE, chromatin immunoprecipitation failed to detect p53 binding to the alphaB-crystallin promoter. These results suggested an indirect mechanism of transactivation involving p53 family members p63 or p73. DeltaNp73 was dramatically induced by p53 in a TAp73-dependent manner, and silencing p73 suppressed the transcriptional activation of alphaB-crystallin by p53. Moreover, ectopic expression of DeltaNp73alpha (but not other p73 isoforms) increased alphaB-crystallin mRNA levels in the absence of p53. Collectively, our results link the molecular chaperone alphaB-crystallin to the cellular genotoxic stress response via a novel mechanism of transcriptional regulation by p53 and p73.

A molecular insight of Hes5-dependent inhibition of myelin gene expression: old partners and new players

This study identifies novel mechanisms of Hes5 function in developmental myelination. We report here upregulation of myelin gene expression in Hes5-/- mice compared to wild-type siblings and downregulation in overexpressing progenitors. This effect was only partially explained by the ability to regulate the levels of Mash1 and bind to N boxes in myelin promoters, as deletion of the DNA-binding domain of Hes5 did not suppress its inhibitory role on myelin gene expression. Novel mechanisms of Hes5 function in the oligodendrocyte lineage include the regulation of feedback loops with the cell-specific transcriptional activator Sox10. In progenitors with low levels of Sox10, Hes5 further decreases the bioavailability of this protein by transcriptional inhibition and direct sequestration of this activator. Increasing levels of Sox10 in progenitors, in turn, bind to Hes5 and titrate out its inhibitory effect by sequestration and displacement of the repressive complexes from myelin promoters. Thus, Hes5-dependent modulation of myelin gene expression involves old players (i.e. Mash1) and novel mechanisms of transcriptional regulation that include cell-specific regulatory loops with transcriptional activators (i.e. Sox10).

Nucleophosmin/B23 regulates transcriptional activation of E2F1 via modulating the promoter binding of NF-κB, E2F1 and pRB

Expression of nucleophosmin/B23 and E2F1 and E2F1-dependent transcription increased in U1 bladder cancer cells upon serum stimulation from quiescence. Nucleophosmin/B23-siRNA treatment abrogated such increase of E2F1-dependent transcriptional activity. In identifying physiologically important factors that may occupy E2F1 promoter and regulate its activity in vivo, we found that the pattern of NF-κB, E2F1 and pRB recruitment to E2F1 promoter changed in a strikingly dynamic fashion as cells progressed from quiescence into serum-stimulated growth. E2F1 promoter activity in quiescent cells was associated with recruitment of NF-κB. NF-κB was replaced largely by E2F1 in concert with gene activation during the early stage (12 h) of serum stimulation. At late stage (24 h) of serum stimulation, pRB was then recruited to the E2F1-promoter complex to counterbalance its activity. Upon siRNA-mediated reduction of intracellular nucleophosmin/B23, E2F1 and pRB were recruited to the promoter with the dissociation of NF-κB concomitant with gene inactivation. Based on immunoprecipitation experiments, nucleophosmin/B23 was found to be associated with NF-κB in cells grown in serum-supplemented but not in serum-deprived medium. Furthermore, nucleophosmin/B23 could also be co-immunoprecipitated with ppRB at the early stage (12 h) but not at the late stage (24 h) of serum stimulation. The results demonstrate a novel mechanism for transcriptional regulation of E2F1 and identify the functional role of nucleophosmin/B23 in modulating the binding of NF-κB, E2F1 and pRB to activate E2F1 promoter.

DNA-looping by RXR Tetramers Permits Transcriptional Regulation “at a Distance”

RXR, a member of the superfamily of nuclear hormone receptors, regulates gene transcription in response to 9-cis-retinoic acid. We previously showed that, among nuclear receptors, RXR is unique in that it self-associates into homotetramers, and that these tetramers dissociate rapidly upon ligation. Here, we report that binding of RXR tetramers to DNA containing two RXR response elements results in a dramatic DNA-looping. RXR can thus juxtapose distant DNA sequences, enabling transcriptional regulation by far-upstream factors. We show that RXR functions as a DNA architectural factor and that, while this activity is regulated by 9-cis-retinoic acid, it is distinct from and independent of the receptor's intrinsic transcriptional activity. The data establish RXR as the first identified architectural factor whose activity is regulated by a small ligand, and demonstrate a novel mechanism of transcriptional regulation by retinoids.

Interaction with GATA transcription factors provides a mechanism for cell-specific effects of c-Fos.

c-Fos is a multifunctional transcription factor that is involved in cellular proliferation, differentiation and apoptosis. c-Fos is rapidly induced by a variety of hormones, growth factors and other extracellular stimuli, resulting in cell-specific responses. One potential mechanism underlying the cell-specific effects of c-Fos may be its ability to regulate gene expression through interaction with tissue-restricted transcription factors. We report here that c-Fos interacts with the cell-specific GATA proteins to potentiate their ability to transactivate target promoters, via GATA-binding sites. c-Fos is recruited to GATA proteins through direct interaction with their N-terminal activation domain. Neither the leucine zipper nor the DNA-binding domain of c-Fos is required for physical interaction with GATA proteins. Instead, a C-terminal domain located between amino acids 235 and 296, which is conserved in FosB but not in the nontransforming Fos family members, FosB/SF or Fra-1, is essential for c-Fos-GATA interaction. These data suggest that c-Fos may act as an inducible cofactor for cell-specific transcription factors and unravel a novel mechanism for transcriptional regulation by c-Fos, independent of the well-studied AP-1 pathway. The results also raise the possibility that dysregulated interaction with cell-specific transcription factors may be an important component in cellular transformation by nuclear oncogenes.

GA-binding protein (GABP) and Sp1 are required, along with retinoid receptors, to mediate retinoic acid responsiveness of CD18 (β2leukocyte integrin): a novel mechanism of transcriptional regulation in myeloid cells

AbstractCD18 (β2leukocyte integrin) is transcriptionally regulated in myeloid cells, but the mechanisms that increase its expression in response to retinoic acid (RA) have not been defined. The CD18 promoter was activated by RA treatment in stably transfected U937 myeloid cells. We identified a retinoic acid response element (RARE) that lies nearly 900 nucleotides upstream of the CD18 transcriptional start site that was bound by the RA receptors, retinoic acid receptor (RAR) and retinoic X receptor (RXR). This RARE accounted for one half of the RA responsiveness of CD18. However, unexpectedly, one half of the dynamic response to RA was mediated by the 96-nucleotide CD18 minimal promoter, which lacks a recognizable RARE. Binding sites for theetstranscription factor, GA-binding protein (GABP), and Sp1 were required for full RA responsiveness of both the CD18 minimal promoter and the full-length promoter. Theetssites conferred RA responsiveness on an otherwise unresponsive heterologous promoter, and RA responsiveness was directly related to the number ofetssites. The transcriptional coactivator p300/CBP physically interacted with GABP in vivo, and p300 increased the responsiveness of the CD18 promoter to RA. These studies demonstrate a novel role for non-RAR transcription factors in mediating RA activation in myeloid cells. They support the concept that transcription factors other than RARs are required for RA-activated gene expression. We hypothesize that a multiprotein complex—an enhanceosome—that includes GABP, other transcription factors, and coactivators, dynamically regulates CD18 expression in myeloid cells.

Ataxin-3 Is a Histone-binding Protein with Two Independent Transcriptional Corepressor Activities

The mechanisms of pathology for the family of polyglutamine disease proteins are unknown; however, recently it was shown that several of these proteins inhibit transcription suggesting that transcriptional repression may be a potential mechanism for pathology. In the present study we use cell transfections, in vitro binding, co-immunoprecipitations, and reporter assays to show that the polyglutamine disease protein, ataxin-3, interacts with the major histone acetyltransferases cAMP-response-element binding protein (CREB)-binding protein, p300, and p300/CREB-binding protein-associated factor and inhibits transcription by these coactivators. Importantly, endogenous ataxin-3 is co-immunoprecipitated with each of these coactivators in non-transfected cells. The C-terminal polyglutamine-containing domain of ataxin-3 inhibits coactivator-dependent transcription and is required for binding coactivators. The N-terminal domain of ataxin-3 inhibits histone acetylation by p300 in vitro and inhibits transcription in vivo. Histone binding and blocking access of coactivators to acetylation sites on histones appears to be the mechanism of inhibition. Together, our data provide a novel mechanism of transcriptional regulation by ataxin-3 that involves targeting histones, coactivators, and an independent mode of direct repression of transcription, and suggests that its physiological function and possibly pathological effects are linked to its interactions with these proteins.