15 results on '"Mauro E"'
Search Results
2. Heterochromatin organization of a natural yeast telomere. Recruitment of Sir3p through interaction with histone H4 N terminus is required for the establishment of repressive structures.
- Author
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Venditti, S, Vega-Palas, M A, and Di Mauro, E
- Abstract
The chromatin organization of eukaryotic telomeres is essential for telomeric function and is currently receiving great attention. In yeast, the structural organization of telomeres involves a complex interplay of telomeric proteins that results in the formation of heterochromatin. This telomeric heterochromatin involves homotypic and heterotypic protein interactions that have been summarized in a general model. Recent analyses have focused on the study of the structural complexity at yeast telomeres to the level of specific nucleosomes and of the distribution of protein complexes in a natural telomeric region (LIII). In this report, we further analyze the structural complexity of LIII and the implication of this structure on telomeric silencing. It is shown that the establishment of repressive heterochromatin structures at LIII requires the recruitment of Sir3p through interaction with the N terminus of histone H4. The establishment of such structures does not require acetylation of any of four lysines located in the H4 N terminus (lysines 5, 8, 12, and 16).
- Published
- 1999
3. Heterochromatin organization of a natural yeast telomere. Changes of nucleosome distribution driven by the absence of Sir3p.
- Author
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Vega-Palas, M A, Venditti, S, and Di Mauro, E
- Abstract
We have defined the in vivo heterochromatin structure of the left telomere of Saccharomyces cerevisiae chromosome III (LIII). Analysis of heterochromatin of a single telomere was so far lacking, due to the difficulties intrinsic to the highly repetitive nature of telomeric sequences. In LIII, the terminal (C1-3A)n repetitive sequences are followed by a complete X element and by the single copy Ty5-1 retrotransposon. Both the telosome and the X element exhibit overall resistance to micrococcal nuclease digestion reflecting their tight chromatin structure organization. The X element contains protein complexes and irregularly distributed but well localized nucleosomes. In contrast, a regular array of phased nucleosomes is associated with the promoter region of Ty5-1 and with the more centromere-proximal sequences. The lack of a structural component of yeast telomeres, the SIR3 protein, does not alter the overall tight organization of the X element but causes a nucleosome rearrangement within the promoter region of Ty5-1 and releases Ty5-1 silencing. Thus, Sir3p links the modification of the heterochromatin structure with loss of transcriptional silencing.
- Published
- 1998
4. Factors affecting Saccharomyces cerevisiae ADH2 chromatin remodeling and transcription.
- Author
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Verdone, L, Cesari, F, Denis, C L, Di Mauro, E, and Caserta, M
- Abstract
The chromatin structure of the Saccharomyces cerevisiae ADH2 gene is modified during the switch from repressing (high glucose) to derepressing (low glucose) conditions of growth. Loss of protection toward micrococcal nuclease cleavage for the nucleosomes covering the TATA box and the RNA initiation sites (-1 and +1, respectively) is the major modification taking place and is strictly dependent on the presence of the transcriptional activator ADR1. To identify separate functions involved in the transition from a repressed to a transcribing promoter, we have analyzed the ADH2 chromatin organization in various genetic backgrounds. Deletion of the CCR4 gene coding for a general transcription factor impaired ADH2 expression without affecting chromatin remodeling. Growing yeast at 37 degrees C also resulted in chromatin remodeling at the ADH2 locus even under glucose repressing conditions. However, although this temperature-induced remodeling was dependent on the ADR1 protein, no ADH2 mRNA was observed. In addition, inactivating RNA polymerase II (and therefore, elongation) was found to have no effect on the ability to reconfigure nucleosomes. Taken together, these data indicate that chromatin remodeling by itself is insufficient to induce transcription at the ADH2 promoter.
- Published
- 1997
5. The intrinsic topological information of the wild-type and of up-promoter mutations of the Saccharomyces cerevisiae alcohol dehydrogenase II regulatory region.
- Author
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Della Seta, F, Camilloni, G, Venditti, S, and Di Mauro, E
- Abstract
A 569-base pair fragment encompassing the upstream regulatory region, the RNA initiation sites, and the initial part of the coding region of the Saccharomyces cerevisiae alcohol dehydrogenase II gene has been analyzed for the presence of sites which undergo conformational modification under torsional stress. Fine mapping of P1 and S1 endonuclease-sensitive sites was obtained on single topoisomers produced by in vitro ligation. It was shown that the upstream activator sequence, the TATA sequence, a region directly upstream to the RNA initiation sites, and several positions in the first segment of the transcribed region change conformation as a function of the applied torsional stress in a precisely coordinate fashion. The superhelical density optima for this coordinate modifications have been determined. Analysis of the conformational changes of the promoter sequence in several naturally occurring (Young, E. T., Williamson, V. M., Taguchi, A., Smith, M., Sledziewski, L., Russel, D., Osterman, J., Denis, C., Cox, D., and Beier, D., (1982) in Genetic Engineering of Microorganisms for Chemicals (Hollander, A., De Moss, R. D., Kaplan, S., Konisky, J., Savage, D., and Wolle, R. S., eds) pp. 335-361, Plenum Publishing Corp., New York) up-promoter constitutive mutants was performed. This analysis has shown that the conformation of functionally relevant sites changes as a function of sequence mutations that have taken place elsewhere; this shows that the conformational behavior of the whole promoter region is linked and suggests transmission in cis of topological effects in RNA polymerase II promoters.
- Published
- 1988
- Full Text
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6. Transitions in topological organization of supercoiled DNA domains as a potential regulatory mechanism.
- Author
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Carnevali, F, Caserta, M, and Di Mauro, E
- Abstract
We present an analysis of the influence of DNA superhelicity on the topology of chimeric plasmids. A correlation is found between topological variations and in vivo/in vitro functions. Data refer to the topological transitions observed in function of variations of the superhelical density in the three closed DNA domains that represent the three extreme examples, from the point of view of the topological organization, among many chimeric systems analyzed. The plasmids studied are ADR2-BS-pBR322 (the vector pBR322 + the yeast gene ADR2), ADR3-5c-yRp7 (containing yeast TRP1, a constitutive mutant of yeast ADR2, a fragment of 5 kilobases of unanalyzed chromosomal DNA and the vector pBR322), and p31 (pBR322 + a yeast DNA fragment encompassing the right moiety of the Ty1 element and its in vivo promoter). In the model systems analyzed, the topological transitions observed in the eukaryotic sequences (relevant in one case for activation of selective in vitro transcription (Ty), in another (ADR2) for the in vivo expression) take place in the range of superhelical densities predicted on theoretical ground (Vologodskii, A. V., Lukashin, A. V. Anshelevich, V. V. & Frank-Kamenetskii, M. D. (1979) Nucleic Acids Res. 6, 967-982).
- Published
- 1984
- Full Text
- View/download PDF
7. Activation of in vitro transcription and topology of closed DNA domains.
- Author
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Di Mauro, E, Caserta, M, Negri, R, and Carnevali, F
- Abstract
Activation of in vitro transcription of otherwise inert DNA sequences by purified yeast RNA polymerase II has been observed following the introduction in closed DNA domains of fragments of various origin. This enhancer-like effect on the in vitro transcriptional capacity is only detected in negatively supercoiled DNA domains and is characterized for each chimaeric plasmid by the superhelical density (- sigma) at which a sharp transition toward activation takes place. We have analyzed the topological state (as defined by localization and evaluation of the relative occurrence of secondary structures sensitive to S1 endonuclease) of the activated closed domains as a function of the conditions that determine the transcriptional enhancer effect, i.e. superhelical density, size, and nature of the components of the domains. We observe that variations in transcriptional capacity coincide with a defined pattern of secondary structures. These observations support a cause-effect relation between topology and regulation of transcription.
- Published
- 1985
- Full Text
- View/download PDF
8. Structure of RNA polymerase II promoters. Coordinate conformational alteration of the upstream activator of the TATA- and RNA-initiation sequences under moderate torsional stress.
- Author
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Camilloni, G, Della Seta, F, Negri, R, and Di Mauro, E
- Abstract
Different conformations of the circular DNA domains containing the intergenic region of the Saccharomyces cerevisiae GAL1-GAL10 divergent genes (914 base pairs) were modified by in vitro ligation in various conditions. The effect of increasing torsional stress on the conformation of the composing elements was determined by analysis of the sensitivity to the single strand-specific S1 endonuclease and it was observed that the sites of conformational alterations correspond to the positions relevant for promoter function (upstream activator sequence, TATA sequence, and RNA initiation site).
- Published
- 1986
- Full Text
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9. Multiple overlapping positions of nucleosomes with single in vivo rotational setting in the Hansenula polymorpha RNA polymerase II MOX promoter.
- Author
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Costanzo, G, Di Mauro, E, Negri, R, Pereira, G, and Hollenberg, C
- Abstract
In vivo nucleotide-level mapping of nucleosomes in the promoter of the methanol oxidase (MOX) gene in the yeast Hansenula polymorpha is reported. The 4 nucleosomes analyzed are organized in families; they localize in alternative positions along a unique rotational phase, and the linker regions can be occupied by alternative nucleosomes. This organization underscores a substantial freedom of choice by histone octamers when nucleating on a promoter region.
- Published
- 1995
10. Generation of long RNA chains in water.
- Author
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Costanzo G, Pino S, Ciciriello F, and Di Mauro E
- Subjects
- Base Sequence, Cyclic AMP chemistry, Cyclic GMP chemistry, Kinetics, Models, Chemical, Molecular Structure, Nucleic Acid Conformation, Oligoribonucleotides chemical synthesis, RNA chemical synthesis, Oligoribonucleotides chemistry, RNA chemistry, Water chemistry
- Abstract
The synthesis of RNA chains from 3',5'-cAMP and 3',5'-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40-90 degrees C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3',5'-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3', 5'-cGMP to approximately 25-nucleotide-long RNA molecules, and of 3',5'-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3',5'-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.
- Published
- 2009
- Full Text
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11. Nonenzymatic RNA ligation in water.
- Author
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Pino S, Ciciriello F, Costanzo G, and Di Mauro E
- Subjects
- Adenine chemistry, Biochemistry methods, Dimerization, Hydrogen-Ion Concentration, Kinetics, Nucleic Acid Conformation, Oligonucleotides chemistry, Penicillium enzymology, Ribonucleases chemistry, Temperature, Thermodynamics, Time Factors, Water chemistry, RNA chemistry
- Abstract
We describe the nonenzymatic ligation of RNA oligomers in water. Dimers and tetramers are formed in a time-, pH-, and temperature-dependent reaction. Ligation efficiency depends on oligonucleotide length and sequence and is strongly enhanced by adenine-based nucleotide cofactors. Ligation of short RNA fragments could have liberated the prebiotic polymerization systems from the thermodynamically demanding task of reaching a (pre)genetically meaningful size by stepwise addition of one precursor monomer at the time.
- Published
- 2008
- Full Text
- View/download PDF
12. Nucleoside phosphorylation by phosphate minerals.
- Author
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Costanzo G, Saladino R, Crestini C, Ciciriello F, and Di Mauro E
- Subjects
- Phosphorylation, Adenosine metabolism, Minerals metabolism, Phosphates metabolism
- Abstract
In the presence of formamide, crystal phosphate minerals may act as phosphate donors to nucleosides, yielding both 5'- and, to a lesser extent, 3'-phosphorylated forms. With the mineral Libethenite the formation of 5'-AMP can be as high as 6% of the adenosine input and last for at least 10(3) h. At high concentrations, soluble non-mineral phosphate donors (KH(2)PO(4) or 5'-CMP) afford 2'- and 2':3'-cyclic AMP in addition to 5'-and 3'-AMP. The phosphate minerals analyzed were Herderite Ca[BePO(4)F], Hureaulite Mn(2+)(5)(PO(3)(OH)(2)(PO(4))(2)(H(2)O)(4), Libethenite Cu(2+)(2)(PO(4))(OH), Pyromorphite Pb(5)(PO(4))(3)Cl, Turquoise Cu(2+)Al(6)(PO(4))(4)(OH)(8)(H(2)O)(4), Fluorapatite Ca(5)(PO(4))(3)F, Hydroxylapatite Ca(5)(PO(4))(3)OH, Vivianite Fe(2+)(3)(PO(4))(2)(H(2)O)(8), Cornetite Cu(2+)(3)(PO(4))(OH)(3), Pseudomalachite Cu(2+)(5)(PO(4))(2)(OH)(4), Reichenbachite Cu(2+)(5)(PO(4))(2)(OH)(4), and Ludjibaite Cu(2+)(5)(PO(4))(2)(OH)(4)). Based on their behavior in the formamide-driven nucleoside phosphorylation reaction, these minerals can be characterized as: 1) inactive, 2) low level phosphorylating agents, or 3) active phosphorylating agents. Instances were detected (Libethenite and Hydroxylapatite) in which phosphorylation occurs on the mineral surface, followed by release of the phosphorylated compounds. Libethenite and Cornetite markedly protect the beta-glycosidic bond. Thus, activated nucleic monomers can form in a liquid non-aqueous environment in conditions compatible with the thermodynamics of polymerization, providing a solution to the standard-state Gibbs free energy change (DeltaG degrees ') problem, the major obstacle for polymerizations in the liquid phase in plausible prebiotic scenarios.
- Published
- 2007
- Full Text
- View/download PDF
13. Origin of informational polymers: differential stability of phosphoester bonds in ribomonomers and ribooligomers.
- Author
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Saladino R, Crestini C, Ciciriello F, Di Mauro E, and Costanzo G
- Subjects
- Adenosine chemistry, Adenosine metabolism, Deoxyribonucleotides chemistry, Deoxyribonucleotides metabolism, Formamides chemistry, Molecular Structure, Phosphates chemistry, Phosphates metabolism, Polymers metabolism, Ribonucleotides metabolism, Polymers chemistry, RNA Stability, Ribonucleotides chemistry
- Abstract
We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the beta-glycosidic and 3'- and 5'-phosphoester bonds. Stabilities were measured under a wide range of temperatures and water/formamide ratios. The stability of phosphodiester bonds in oligoribonucleotides was determined in the same environments. The comparison of bond stabilities in the monomer versus the polymer forms of the ribo compounds revealed that physico-chemical conditions exist in which polymerization is thermodynamically favored. These conditions were compared with those determining a similar behavior for 2'-deoxyribonucleosides, deoxyribonucleotides, and deoxyribooligonucleotides and were shown to profoundly differ. The implications of these facts on the origin of informational polymers are discussed.
- Published
- 2006
- Full Text
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14. Origin of informational polymers. Differential stability of 3'- and 5'-phosphoester bonds in deoxy monomers and oligomers.
- Author
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Saladino R, Crestini C, Busiello V, Ciciriello F, Costanzo G, and Di Mauro E
- Subjects
- Base Sequence, Catalysis, Chromatography, High Pressure Liquid, DNA chemistry, Deoxyadenosines chemistry, Formamides chemistry, Glycosides chemistry, Kinetics, Lipids chemistry, Macromolecular Substances chemistry, Models, Chemical, Molecular Sequence Data, Molecular Structure, Nucleotides chemistry, Oligonucleotides chemistry, RNA chemistry, Temperature, Time Factors, Biotechnology methods, Esters chemistry, Polymers chemistry
- Abstract
To survive, an informational macromolecule must solve the major problem set by its very polymeric nature: instability. This is especially true in prebiotic terms because of the presumed initial absence of protective structures (proteins, lipids, etc.). We have analyzed the stability of the beta-glycosidic and of the 3'- and 5'-phosphoester bonds in both deoxy monomers and deoxy oligomers under a large set of conditions. The results show a strong dependence of the relative stability of these bonds on the physico-chemical environment. A set of conditions has been identified in which the stability of polymers becomes comparable with that of the precursor monomers. In certain instances the stability of the 5'-phosphoester bond is even higher in the polymer than in the mononucleotide.
- Published
- 2005
- Full Text
- View/download PDF
15. In vivo changes of nucleosome positioning in the pretranscription state.
- Author
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Di Mauro E, Verdone L, Chiappini B, and Caserta M
- Subjects
- Blotting, Northern, Catalysis, Chromatin metabolism, DNA-Binding Proteins chemistry, Models, Genetic, Nucleosomes metabolism, Peptides chemistry, Plasmids metabolism, Protein Structure, Tertiary, RNA metabolism, RNA, Messenger metabolism, Temperature, Transcription Factors chemistry, Nucleosomes chemistry, Nucleosomes physiology, Promoter Regions, Genetic, Saccharomyces cerevisiae genetics, Saccharomyces cerevisiae Proteins, Transcription, Genetic
- Abstract
The involvement of chromatin structure and organization in transcriptional regulatory pathways has become evident. One unsolved question concerns the molecular mechanisms of chromatin remodeling during in vivo promoter activation. By using a high resolution in vivo analysis we show that when yeast cells are exposed to a regulatory signal the positions of specific nucleosomes change. The system analyzed consists of the basic elements of the Saccharomyces cerevisiae ADH2 promoter, two nucleosomes of which are shown to change the distribution of their positions by few nucleotides in the direction of transcription when the glucose content of the medium is lowered. Such repositioning does not occur in the absence of the ADH2 transcriptional activator Adr1 or in the presence of its DNA-binding domain alone. A construct consisting of the DNA-binding domain plus a 43-amino acid peptide containing the Adr1 activation domain is sufficient to induce the same effect of the full-length protein. Nucleosome repositioning occurs even when the catalytic activity of the RNA polymerase II is impaired, suggesting that the Adr1 activation domain mediates the recruitment of some factor to correctly preset the relevant sequences for the subsequent transcription steps.
- Published
- 2002
- Full Text
- View/download PDF
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