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  • 1
    Electronic Resource
    Electronic Resource
    The role of histones and their modifications in the informative content of chromatin (1993)
    Springer
    Cellular and molecular life sciences 49 (1993), S. 780-788 
    Details
    ISSN: 1420-9071
    Keywords: Chromatin ; epigenetic mechanism ; histone acetylation ; imprinting ; nucleosome
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract It is traditionally accepted that the DNA sequence cannot by itself explain all the mechanisms necessary for the development of living beings, especially in eukaryotes. Indeed part of the information used in these processes is stored in other ways, generally called ‘epigenetic’, whose molecular mechanisms are mostly unknown. The ultimate explanation for them might reside in the non-DNA moiety of chromatin which may play an active role in heredity (‘chromatin information’). Histones are the universal structural component of chromatin. However, recent studies strongly suggest that histones, and their modifications — especially the reversible acetylation of lysines — may act as a recognition signal for regulatory proteins and they may participate, for this reason, in gene regulation. This type of information could be maintained through its replication and, ultimately, it could form the molecular basis of certain processes related to the development of the eukaryotic organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01923548
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis of the thiolase family. Implications for the evolutionary origin of peroxisomes (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 147-155 
    Details
    ISSN: 1432-1432
    Keywords: Thiolase ; Peroxisome evolution ; Bootstrap analysis ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The thiolase family is a widespread group of proteins present in prokaryotes and three cellular compartments of eukaryotes. This fact makes this family interesting in order to study the evolutionary process of eukaryotes. Using the sequence of peroxisomal thiolase from Saccharomyces cerevisiae recently obtained by us and the other known thiolase sequences, a phylogenetic analysis has been carried out. It shows that all these proteins derived from a primitive enzyme, present in the common ancestor of eubacteria and eukaryotes, which evolved into different specialized thiolases confined to various cell compartments. The evolutionary tree obtained is compatible with the endosymbiotic theory for the origin of peroxisomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00183226
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  • 3
    Electronic Resource
    Electronic Resource
    Chromatin structure of the 5′ flanking region of the yeastLEU2 gene (1989)
    Springer
    Molecular genetics and genomics 217 (1989), S. 464-470 
    Details
    ISSN: 1617-4623
    Keywords: Nucleosome positioning ; LEU2 gene ; Saccharomyces cerevisiae ; tRNA3 Leu gene ; Chromatin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The chromatin structure of theLEU2 gene and its flanks has been studied by means of nuclease digestion, both with micrococcal nuclease and DNase I. The gene is organized in an array of positioned nucleosomes. Within the promoter region, the nucleosome positioning places the regulatory sequences, putative TATA box and upstream activator sequence outside the nucleosomal cores. The tRNA3 Leu gene possesses a characteristic structure and is protected against nucleases. Most of the 5′ flank is sensitive to DNase I digestion, although no clear hypersensitive sites were found. The chromatin structure is independent of either the transcriptional state of the gene or the chromosomal or episomal location. Finally, in the plasmid pJDB207, which lacks most of the promoter, we have found that the chromatin structure of the coding region is similar to that of the wild-type allele.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02464918
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  • 4
    Electronic Resource
    Electronic Resource
    Sequencing analysis of a 4·1 kb subtelomeric region from yeast chromosome IV identifies HXT15, a new member of the hexose transporter familyM.B. and D.S. contributed equally to his paper. (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 12 (1996), S. 1005-1011 
    Details
    ISSN: 0749-503X
    Keywords: genome sequencing ; Saccharomyces cerevisiae ; yeast ; chromosome IV ; HXT15 ; hexose transporter ; Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The DNA sequence of a 4·1 kb region of Saccharomyces cerevisiae chromosome IV was determined. This region contains a single open reading frame which codes for a member of the hexose transporter family. This new gene has been named HXT15 according to yeast gene data bases. The sequence has been entered in the EMBL data library under Accession Number X92891.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 5
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    Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-24
    Description: The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo influence of positioned nucleosomes on transcription elongation. The particular features at the 5' end and around the polyadenylation site indicate that this polymerase undergoes extensive specific-activity regulation in the initial and final transcription elongation phases. The genes encoding for ribosomal proteins show distinctive features at both ends. BioGRO also provides the first nascentome analysis for RNA polymerase III, which indicates that transcription of tRNA genes is poorly regulated at the individual copy level. The present study provides a novel perspective of the transcription cycle that incorporates inactivation/reactivation as an important aspect of RNA polymerase dynamics.
    Keywords: Massively Parallel (Deep) Sequencing, Transcriptome Mapping - Monitoring Gene Expression
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-22
    Description: Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available applications for comparative microarray analysis exclusively focus on changes in gene expression within known transcribed regions of predicted protein-coding genes, the changes that occur in non-predictable genetic elements, such as non-coding RNAs. Here, we present a web application for the visualization of strand-specific tiling microarray or next-generation sequencing data that allows customized detection of differentially expressed regions all along the genome in an unspecific manner, that allows identification of all RNA sequences, predictable or not. Availability and implementation: The web application is freely accessible at http://tilingscan.uv.es/ . TilingScan is implemented in PHP and JavaScript. Contact: vicente.arnau@uv.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    The role of histones and their modifications in the informative content of chromatin (1993)
    Springer
    Details
    Publication Date: 1993-09-01
    Print ISSN: 0014-4754
    Topics: Biology , Medicine
    Published by Springer
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  • 8
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    The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-06
    Description: We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within the heterogeneity of a wild-type cell population growing in optimal conditions. The transcriptomic analysis of sorted microcolonies confirmed that the growth rate dictates alternative expression programs by modulating transcription and mRNA decay. The regulation of overall mRNA turnover keeps a constant ratio between mRNA decay and the dilution of [mRNA] caused by cellular growth. This regulation minimizes the indiscriminate transmission of mRNAs from mother to daughter cells, and favors the response capacity of the latter to physiological signals and environmental changes. We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Topoisomerase II regulates yeast genes with singular chromatin architectures (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-02
    Description: Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes, whereas topo IIβ regulates developmental genes in conjunction with chromatin remodeling and heterochromatin transitions. Here we show that in budding yeast, topo II regulates the expression of specific gene subsets. To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II. We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II. These genes present distinctive functional and structural traits in comparison with the genome average. Yeast topo II is a positive regulator of genes with well-defined promoter architecture that associates to chromatin remodeling complexes; it is a negative regulator of genes extremely hypo-acetylated with complex promoters and undefined nucleosome positioning, many of which are involved in polyamine transport. These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    mRNAStab--a web application for mRNA stability analysis (2013)
    Oxford University Press
    Details
    Publication Date: 2013-03-15
    Description: Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at http://mRNAStab.uv.es/ . mRNAStab is written in C, PHP and R. Contact: vicente.arnau@uv.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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