Showing papers on "Upstream activating sequence published in 2013"

Far upstream element binding protein 1: a commander of transcription, translation and beyond.

Abstract: The far upstream binding protein 1 (FBP1) was first identified as a DNA-binding protein that regulates c-Myc gene transcription through binding to the far upstream element (FUSE) in the promoter region 1.5 kb upstream of the transcription start site. FBP1 collaborates with TFIIH and additional transcription factors for optimal transcription of the c -Myc gene. In recent years, mounting evidence suggests that FBP1 acts as an RNA-binding protein and regulates mRNA translation or stability of genes, such as GAP43, p27Kip and nucleophosmin. During retroviral infection, FBP1 binds to and mediates replication of RNA from Hepatitis C and Enterovirus 71. As a nuclear protein, FBP1 may translocate to the cytoplasm in apoptotic cells. The interaction of FBP1 with p38/JTV-1 results in FBP1 ubiquitination and degradation by the proteasomes. Transcriptional and post-transcriptional regulations by FBP1 contribute to cell proliferation, migration or cell death. FBP1 association with carcinogenesis has been reported in c-Myc dependent or independent manner. This review summarizes biochemical features of FBP1, its mechanism of action, FBP family members and the involvement of FBP1 in carcinogenesis.

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity

Abstract: The core promoter is the region in which RNA polymerase II is recruited to the DNA and acts to initiate transcription, but the extent to which the core promoter sequence determines promoter activity levels is largely unknown. Here, we identified several base content and k-mer sequence features of the yeast core promoter sequence that are highly predictive of maximal promoter activity. These features are mainly located in the region 75 bp upstream and 50 bp downstream of the main transcription start site, and their associations hold for both constitutively active promoters and promoters that are induced or repressed in specific conditions. Our results unravel several architectural features of yeast core promoters and suggest that the yeast core promoter sequence downstream of the TATA box (or of similar sequences involved in recruitment of the pre-initiation complex) is a major determinant of maximal promoter activity. We further show that human core promoters also contain features that are indicative of maximal promoter activity; thus, our results emphasize the important role of the core promoter sequence in transcriptional regulation.

Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo

Abstract: Mediator is a prominent multisubunit coactivator that functions as a bridge between gene-specific activators and the basal RNA polymerase (Pol) II initiation machinery. Here, we study the poorly documented role of Mediator in basal, or activator-independent, transcription in vivo. We show that Mediator is still present at the promoter when the Pol II machinery is recruited in the absence of an activator, in this case through a direct fusion between a basal transcription factor and a heterologous DNA binding protein bound to the promoter. Moreover, transcription resulting from activator-independent recruitment of the Pol II machinery is impaired by inactivation of the essential Mediator subunit Med17 due to the loss of Pol II from the promoter. Our results strongly support that Mediator is an integral component of the minimal machinery essential in vivo for stable Pol II association with the promoter.

Self-association of the Gal4 inhibitor protein Gal80 is impaired by Gal3: evidence for a new mechanism in the GAL gene switch.

Abstract: The DNA-binding transcriptional activator Gal4 and its regulators Gal80 and Gal3 constitute a galactose-responsive switch for the GAL genes of Saccharomyces cerevisiae. Gal4 binds to GAL gene UASGAL (upstream activation sequence in GAL gene promoter) sites as a dimer via its N-terminal domain and activates transcription via a C-terminal transcription activation domain (AD). In the absence of galactose, a Gal80 dimer binds to a dimer of Gal4, masking the Gal4AD. Galactose triggers Gal3-Gal80 interaction to rapidly initiate Gal4-mediated transcription activation. Just how Gal3 alters Gal80 to relieve Gal80 inhibition of Gal4 has been unknown, but previous analyses of Gal80 mutants suggested a possible competition between Gal3-Gal80 and Gal80 self-association interactions. Here we assayed Gal80-Gal80 interactions and tested for effects of Gal3. Immunoprecipitation, cross-linking, and denaturing and native PAGE analyses of Gal80 in vitro and fluorescence imaging of Gal80 in live cells show that Gal3-Gal80 interaction occurs concomitantly with a decrease in Gal80 multimers. Consistent with this, we find that newly discovered nuclear clusters of Gal80 dissipate in response to galactose-triggered Gal3-Gal80 interaction. We discuss the effect of Gal3 on the quaternary structure of Gal80 in light of the evidence pointing to multimeric Gal80 as the form required to inhibit Gal4.

Regulation of entry into gametogenesis by Ste11: the endless game

Abstract: Sexual reproduction is a fundamental aspect of eukaryotic cells, and a conserved feature of gametogenesis is its dependency on a master regulator. The ste11 gene was isolated more than 20 years ago by the Yamamoto laboratory as a suppressor of the uncontrolled meiosis driven by a pat1 mutant. Numerous studies from this laboratory and others have established the role of the Ste11 transcription factor as the master regulator of the switch between proliferation and differentiation in fission yeast. The transcriptional and post-transcriptional controls of ste11 expression are intricate, but most are not redundant. Whereas the transcriptional controls ensure that the gene is transcribed at a high level only when nutrients are rare, the post-transcriptional controls restrict the ability of Ste11 to function as a transcription factor to the G1-phase of the cell cycle from where the differentiation programme is initiated. Several feedback loops ensure that the cell fate decision is irreversible. The complete panel of molecular mechanisms operating to warrant the timely expression of the ste11 gene and its encoded protein basically mirrors the advances in the understanding of the numerous ways by which gene expression can be modulated. Abbreviations: CTD, C-terminal domain; HMG, high-mobility group; MAPK, mitogen-activated protein kinase; PKA, cAMP-dependent protein kinase; SAGA, Spt–Ada–Gcn5–acetyltransferase; Tor, target of rapamycin; TORC1, target of rapamycin complex 1; UASst, upstream activating sequence for ste11

Lack of Robustness of Life Extension Associated With Several Single-Gene P Element Mutations in Drosophila melanogaster

Abstract: The hypothesis tested in this study was that single-gene mutations found previously to extend the life span of Drosophila melanogaster could do so consistently in both long-lived y w and standard w (1118) genetic backgrounds. GAL4 drivers were used to express upstream activation sequence (UAS)-responder transgenes globally or in the nervous system. Transgenes associated with oxidative damage prevention (UAS-hSOD1 and UAS-GCLc) or removal (EP-UAS-Atg8a and UAS-dTOR (FRB) ) failed to increase mean life spans in any expression pattern in either genetic background. Flies containing a UAS-EGFP-bMSRA (C) transgene associated with protein repair were found not to exhibit life extension or detectable enhanced green fluorescent protein (EGFP) activity. The presence of UAS-responder transgenes was confirmed by PCR amplification and sequencing at the 5' and 3' end of each insertion. These results cast doubt on the robustness of life extension in flies carrying single-gene mutations and suggest that the effects of all such mutations should be tested independently in multiple genetic backgrounds and laboratory environments.

MUSCLE-SPECIFIC OVEREXPRESSION OF THE CATALYTIC SUBUNIT OF DNA POLYMERASE γ INDUCES PUPAL LETHALITY IN Drosophila melanogaster

Abstract: We show the physiological effects and molecular characterization of overexpression of the catalytic core of mitochondrial DNA (mtDNA) polymerase (pol γ-α) in muscle of Drosophila melanogaster. Muscle-specific overexpression of pol γ-α using the UAS/GAL4 (where UAS is upstream activation sequence) system produced more than 90% of lethality at the end of pupal stage at 25°C, and the survivor adult flies showed a significant reduction in life span. The survivor flies displayed a decreased mtDNA level that is accompanied by a corresponding decrease in the levels of the nucleoid-binding protein mitochondrial transcription factor A (mtTFA). Furthermore, an increase in apoptosis is detected in larvae and adults overexpressing pol γ-α. We suggest that the pupal lethality and reduced life span of survivor adult flies are both caused mainly by massive apoptosis of muscle cells induced by mtDNA depletion.

Small rna, preparation method therefor and application thereof in pharmaceuticals for specifically up-regulating gene transcriptional activity

Abstract: Disclosed in the present invention are a method for specifically up-regulating gene expression through a target core promoter using small RNAs (including microRNAs and small interfering RNAs), and a series of regulation target genes. The present invention sets forth that when a TATA box sequence is contained in the promoter, a target site is in a range defined by upstream extension of 20 bases from and downstream extension of 20 bases from the TATA box sequence serving as a center; when no TATA box sequence is contained in the promoter, the target site is an upstream sequence of 1-50 with respect to the genetic transcription starting site. The microRNAs hsa-let-7i, hsa-miR-138, hsa-miR-92a, hsa-let-7c and hsa-miR-181d specifically up-regulate the expression of interleukin-2, insulin, thyrocalcitonin, histone and c-myc gene, respectively. Besides, in regard of randomly selected 19 gene promoters, the artificially-synthesized small interfering RNAs (siRNAs) can enhance the transcriptional activities of 78.9% of the genes. An objective of the present invention is to provide a method for specifically up-regulating gene expression using micro-RNAs, and the present invention possesses a high application value and a broad application prospect in the fields of biotechnology and biomedicine.

Novel insights into the epigenetic regulation of Plasmodium falciparum virulence genes

Abstract: Plasmodium falciparum malaria still places a major health burden upon the developing world. The high virulence of this parasite is linked to the variegated expression of single P. falciparum erythrocyte membrane protein 1 (PfEMP1) variants that are encoded by the var gene family. Most vars and other virulence genes implicated in host-parasite interactions are found within transcriptionally inert chromatin domains at the nuclear periphery and are associated with heterochromatin protein 1 (PfHP1). Mutually exclusive gene activation relies on the escape of a single var locus from this repressive environment into a transcriptionally competent perinuclear zone and non-coding elements play an essential role in this process. The exact mechanisms involved in singular gene choice, however, remain elusive. Using a transfection-based approach we identified cis-acting regulatory promoter elements, namely an upstream activating sequence and a mutual exclusion element (MEE), which are essential for var gene induction and singular locus recognition, respectively. Interestingly, in absence of the MEE, active var promoters are no longer introduced into the mutual exclusion programme. A yet unknown nuclear factor binds specifically to the MEE and I consider this interaction to be a prime candidate for the regulation of singular var activity. In addition, the MEE regulates PfEMP1 expression post-transcriptionally. On the mRNA level, this element is able to drastically reduce translation in an autonomous manner. In an independent project, I generated a conditional PfHP1 loss-of-function mutant to functionally characterise this epigenetic regulator. After inducing PfHP1 depletion during early intra-erythrocytic development, parasites progress normally through schizogony but do not enter mitosis in the subsequent generation. Detailed analysis of these PfHP1-deprived parasites revealed four striking phenotypes: (1) they show a massive de-repression of PfHP1-controlled virulence genes, including the entire var repertoire; (2) over 50% of the cells in the parasite population represent viable early stage gametocytes that complete sexual development in absence of PfHP1; (3) this high conversion rate is linked to the induction of an apiap2 TF family member during schizogony of the previous cell cycle; (4) the non-gametocyte cells represent asexual parasites that are reversibly arrested prior to enter S-phase and mitosis. We could thus identify essential roles for PfHP1 in gene silencing, cell cycle progression and showed for the first time that the mechanism of sexual conversion involves a strong epigenetic component.