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  • 1
    Article
    Article
    2009
    ISSN: 1420-682X 
    Language: English
    In: Cellular and molecular life sciences : CMLS, 2009-10-27, Vol.67 (4), p.569-579
    Description: Next-generation sequencing technologies are now being exploited not only to analyse static genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these powerful and rapidly evolving technologies have only been available for a couple of years, they are already making substantial contributions to our understanding of genome expression and regulation. Here, we briefly describe technical issues accompanying RNA-seq data generation and analysis, highlighting differences to array-based approaches. We then review recent biological insight gained from applying RNA-seq and related approaches to deeply sample transcriptomes in different cell types or physiological conditions. These approaches are providing fascinating information about transcriptional and post-transcriptional gene regulation, and they are also giving unique insight into the richness of transcript structures and processing on a global scale and at unprecedented resolution.
    Subject(s): Analysis ; Animals ; Anopheles ; Biochemistry ; Biomedical and Life Sciences ; Biomedicine ; Biotechnology ; Cell Biology ; Data processing ; Gene expression ; Gene Expression Regulation ; general ; Genome ; Genomics ; High-throughput sequencing ; Humans ; Life Sciences ; Mice ; Molecular biology ; Non-coding RNA ; Oligonucleotide Array Sequence Analysis - methods ; Post-transcriptional control ; Review ; Ribonucleic acid ; RNA ; Sequence Analysis, RNA - methods ; Splicing ; Transcription, Genetic ; Transcriptional control ; Transcriptome
    ISSN: 1420-682X
    E-ISSN: 1420-9071
    Source: Alma/SFX Local Collection
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  • 2
    Language: English
    In: Cell, 2012-10-26, Vol.151 (3), p.671-683
    Description: Data on absolute molecule numbers will empower the modeling, understanding, and comparison of cellular functions and biological systems. We quantified transcriptomes and proteomes in fission yeast during cellular proliferation and quiescence. This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions. The integrated data set supports quantitative biology and affords unique insights into cell regulation. Although mRNAs are typically expressed in a narrow range above 1 copy/cell, most long, noncoding RNAs, except for a distinct subset, are tightly repressed below 1 copy/cell. Cell-cycle-regulated transcription tunes mRNA numbers to phase-specific requirements but can also bring about more switch-like expression. Proteins greatly exceed mRNAs in abundance and dynamic range, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume. [Display omitted] ▸ Cellular numbers for all RNAs and most proteins during proliferation and quiescence ▸ Cells contain 1-10 copies of most mRNAs and ∼100–1 million copies of most proteins ▸ Distinct subset of long noncoding RNAs is expressed above 1 copy/cell ▸ Quiescent cells show ∼4-fold lower RNA concentrations and highly remodeled proteome Quantitative RNA-seq and mass spectrometry in two cellular states are used to show that proteins greatly exceed mRNAs in abundance and dynamic range in yeast, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but in contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume.
    Subject(s): Analysis ; Cell Cycle ; Genetic transcription ; Mass Spectrometry - methods ; Messenger RNA ; Physiological aspects ; Proteins ; Proteome - analysis ; Resource ; RNA, Fungal - analysis ; RNA, Long Noncoding - analysis ; RNA, Messenger - analysis ; Schizosaccharomyces - chemistry ; Schizosaccharomyces - cytology ; Schizosaccharomyces - genetics ; Schizosaccharomyces - physiology ; Schizosaccharomyces pombe Proteins - analysis ; Sequence Analysis, RNA - methods ; Transcriptome ; Universities and colleges
    ISSN: 0092-8674
    E-ISSN: 1097-4172
    Source: Backfile Package - All of Back Files EBS [ALLOFBCKF]
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  • 3
    Language: English
    In: Nature communications, 2017-01-24, Vol.8 (1), p.14061-14061
    Description: Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases.
    Subject(s): Chromosome Inversion - genetics ; Chromosomes, Fungal - genetics ; DNA Copy Number Variations - genetics ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; Genome, Fungal - genetics ; Quantitative Trait, Heritable ; Reproductive Isolation ; Schizosaccharomyces - genetics ; Translocation, Genetic - genetics
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    Source: Nature Open Access
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 4
    Language: English
    In: Nucleic acids research, 2019-01-08, Vol.47 (D1), p.D821-D827
    Description: Abstract PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive data coverage with ease of use. The default view now uses ontology structure to provide a concise, non-redundant summary that can be expanded to reveal underlying details and metadata. The phenotype annotation display also offers filtering options to allow users to focus on specific areas of interest. An instance of the JBrowse genome browser has been integrated, facilitating loading of and intuitive access to, genome-scale datasets. Taken together, the new data and pages, along with improvements in annotation display and querying, allow users to probe connections among different types of data to form a comprehensive view of fission yeast biology. The new PomBase implementation also provides a rich set of modular, reusable tools that can be deployed to create new, or enhance existing, organism-specific databases.
    Subject(s): Biochemistry & Molecular Biology ; Database Issue ; Databases, Genetic ; Genome, Fungal - genetics ; Internet ; Life Sciences & Biomedicine ; Schizosaccharomyces - genetics ; Science & Technology ; Software ; User-Computer Interface
    ISSN: 0305-1048
    E-ISSN: 1362-4962
    Source: Web of Science - Science Citation Index Expanded - 2019〈img src="http://exlibris-pub.s3.amazonaws.com/fromwos-v2.jpg" /〉
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 5
    Language: English
    In: Nucleic acids research, 2008-01, Vol.36 (suppl-1), p.D637-D640
    Description: The Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for both the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database, Flybase and Entrez Gene. Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction.
    Subject(s): Animals ; Caenorhabditis elegans - genetics ; Caenorhabditis elegans - metabolism ; Database Management Systems ; Databases, Genetic ; Drosophila melanogaster - genetics ; Drosophila melanogaster - metabolism ; Gene Regulatory Networks ; Humans ; Internet ; Mice ; Protein Interaction Mapping ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae Proteins - metabolism ; Schizosaccharomyces - genetics ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - metabolism ; User-Computer Interface
    ISSN: 0305-1048
    E-ISSN: 1362-4962
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 6
    Article
    Article
    2012
    ISSN: 0168-9525 
    Language: English
    In: Trends in genetics, 2012, Vol.28 (11), p.560-565
    Description: Cell size is highly variable; cells from various tissues differ in volume over orders of magnitudes, from tiny lymphocytes to giant neurons, and cells of a given type change size during the cell cycle. Larger cells need to produce and maintain higher amounts of RNA and protein to sustain biomass and function, although the genome content often remains constant. Available data indicate that the transcriptional and translational outputs scale with cell size at a genome-wide level, but how such remarkably coordinated regulation is achieved remains largely mysterious. With global and systems-level approaches becoming more widespread and quantitative, it is worth revisiting this fascinating problem. Here, we outline current knowledge of the fundamental relations between genome regulation and cell size, and highlight the biological implications and potential mechanisms of the global tuning of gene expression to cellular volume.
    Subject(s): Animals ; Biological and medical sciences ; cell growth ; Cell Size ; Fundamental and applied biological sciences. Psychology ; Gene Expression ; gene regulation ; Genes ; Genetic transcription ; Genetics of eukaryotes. Biological and molecular evolution ; Genome ; Genomes ; Genomics ; Humans ; Medical Education ; Molecular and cellular biology ; transcription ; Transcription Factors - metabolism ; Transcription, Genetic ; yeast
    ISSN: 0168-9525
    Source: Backfile Package - All of Back Files EBS [ALLOFBCKF]
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  • 7
    Language: English
    In: Aging cell, 2013-08, Vol.12 (4), p.563-573
    Description: Summary Target of rapamycin complex 1 (TORC1) is implicated in growth control and aging from yeast to humans. Fission yeast is emerging as a popular model organism to study TOR signaling, although rapamycin has been thought to not affect cell growth in this organism. Here, we analyzed the effects of rapamycin and caffeine, singly and combined, on multiple cellular processes in fission yeast. The two drugs led to diverse and specific phenotypes that depended on TORC1 inhibition, including prolonged chronological lifespan, inhibition of global translation, inhibition of cell growth and division, and reprograming of global gene expression mimicking nitrogen starvation. Rapamycin and caffeine differentially affected these various TORC1‐dependent processes. Combined drug treatment augmented most phenotypes and effectively blocked cell growth. Rapamycin showed a much more subtle effect on global translation than did caffeine, while both drugs were effective in prolonging chronological lifespan. Rapamycin and caffeine did not affect the lifespan via the pH of the growth media. Rapamycin prolonged the lifespan of nongrowing cells only when applied during the growth phase but not when applied after cells had stopped proliferation. The doses of rapamycin and caffeine strongly correlated with growth inhibition and with lifespan extension. This comprehensive analysis will inform future studies into TORC1 function and cellular aging in fission yeast and beyond.
    Subject(s): Aging ; Analysis ; Caffeine ; Caffeine - pharmacology ; Cell growth ; Cell Proliferation ; chronological aging ; Culture Media - metabolism ; Gene expression ; Gene Expression Regulation, Fungal ; gene regulation ; Genes ; Genes, Fungal ; Genetic research ; Hydrogen-Ion Concentration ; Mechanistic Target of Rapamycin Complex 1 ; Microbial Sensitivity Tests ; Microbial Viability - drug effects ; Multiprotein Complexes - antagonists & inhibitors ; Multiprotein Complexes - genetics ; Nitrogen - metabolism ; Original ; Phenotype ; Phosphatidylinositol 3-Kinases - genetics ; Phosphatidylinositol 3-Kinases - metabolism ; Protein Biosynthesis ; Rapamycin ; Schizosaccharomyces - drug effects ; Schizosaccharomyces - growth & development ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Signal Transduction ; Sirolimus - pharmacology ; Target of Rapamycin ; Time Factors ; TOR Serine-Threonine Kinases - antagonists & inhibitors ; TOR Serine-Threonine Kinases - genetics ; translation ; Yeast
    ISSN: 1474-9718
    E-ISSN: 1474-9726
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    Source: Wiley-Blackwell Full Collection 2014
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  • 8
    Language: English
    In: The EMBO journal, 2006-11-01, Vol.25 (21), p.5171-5179
    Description: Eukaryotic DNA replication is initiated from multiple origins of replication, but little is known about the global regulation of origins throughout the genome or in different types of cell cycles. Here, we identify 401 strong origins and 503 putative weaker origins spaced in total every 14 kb throughout the genome of the fission yeast Schizosaccharomyces pombe. The same origins are used during premeiotic and mitotic S‐phases. We found that few origins fire late in mitotic S‐phase and that activating the Rad3 dependent S‐phase checkpoint by inhibiting DNA replication had little effect on which origins were fired. A genome‐wide analysis of eukaryotic origin efficiencies showed that efficiency was variable, with large chromosomal domains enriched for efficient or inefficient origins. Average efficiency is twice as high during mitosis compared with meiosis, which can account for their different S‐phase lengths. We conclude that there is a continuum of origin efficiency and that there is differential origin activity in the mitotic and meiotic cell cycles.
    Subject(s): Cell cycle ; Cell division ; Chromosomes, Fungal - genetics ; Deoxyribonucleic acid ; DNA ; DNA replication ; DNA Replication - genetics ; fission yeast ; Genome, Fungal ; Genomics ; Meiosis - genetics ; microarray analysis ; Replication Origin ; S Phase - genetics ; Schizosaccharomyces - genetics ; Schizosaccharomyces pombe ; Yeast
    ISSN: 0261-4189
    E-ISSN: 1460-2075
    Source: HighWire Press (Free Journals)
    Source: PubMed Central
    Source: Get It Now
    Source: Wiley-Blackwell Full Collection 2014
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  • 9
    Language: English
    In: Nature reviews. Drug discovery, 2008-08, Vol.9 (8), p.583-593
    Description: Organisms are constantly exposed to a wide range of environmental changes, including both short-term changes during their lifetime and longer-term changes across generations. Stress-related gene expression programmes, characterized by distinct transcriptional mechanisms and high levels of noise in their expression patterns, need to be balanced with growth-related gene expression programmes. A range of recent studies give fascinating insight into cellular strategies for keeping gene expression in tune with physiological needs dictated by the environment, promoting adaptation to both short- and long-term environmental changes. Not only do organisms show great resilience to external challenges, but emerging data suggest that they also exploit these challenges to fuel phenotypic variation and evolutionary innovation.
    Subject(s): Adaptation, Biological - genetics ; Animals ; Biological and medical sciences ; Biological Evolution ; Circadian Rhythm - genetics ; Circadian Rhythm - physiology ; Environment ; Fundamental and applied biological sciences. Psychology ; Gene expression ; Gene Expression Regulation - physiology ; Genetic variation ; Genetics of eukaryotes. Biological and molecular evolution ; Growth and Development - genetics ; Growth and Development - physiology ; Homeostasis - genetics ; Homeostasis - physiology ; Humans ; Models, Biological ; Research ; Stress (Psychology) ; Stress, Physiological - genetics ; Time Factors ; Transcription, Genetic - physiology
    ISSN: 1471-0056
    ISSN: 1474-1784
    E-ISSN: 1471-0064
    E-ISSN: 1474-1784
    Source: Academic Search Ultimate
    Source: Nature Journals Online
    Source: Nature Reviews
    Source: Get It Now
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  • 10
    Language: English
    In: PloS one, 2016, Vol.11 (3), p.e0151102
    Description: At present, wine is generally produced using Saccharomyces yeast followed by Oenococus bacteria to complete malolactic fermentation. This method has some unsolved problems, such as the management of highly acidic musts and the production of potentially toxic products including biogenic amines and ethyl carbamate. Here we explore the potential of the fission yeast Schizosaccharomyces pombe to solve these problems. We characterise an extensive worldwide collection of S. pombe strains according to classic biochemical parameters of oenological interest. We identify three genetically different S. pombe strains that appear suitable for winemaking. These strains compare favourably to standard Saccharomyces cerevisiae winemaking strains, in that they perform effective malic acid deacidification and significantly reduce levels of biogenic amines and ethyl carbamate precursors without the need for any secondary bacterial malolactic fermentation. These findings indicate that the use of certain S. pombe strains could be advantageous for winemaking in regions where malic acid is problematic, and these strains also show superior performance with respect to food safety.
    Subject(s): Acids ; Alcohol ; Amines ; Amino acids ; Bacteria ; Baking yeast ; Biogenic amines ; Biology and Life Sciences ; Chemistry ; Ethyl carbamate ; Eukaryotes ; Fermentation ; Food safety ; Food science ; Genetic aspects ; Glucose ; Glycerol ; Laboratories ; Malic acid ; Malolactic fermentation ; Medicine and Health Sciences ; Metabolism ; Metabolites ; Methods ; Nuclear engineering ; Nuclear safety ; Parameter identification ; Physical Sciences ; Properties ; Research ; Research and Analysis Methods ; Saccharomyces ; Schizosaccharomyces - classification ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Species Specificity ; Strains (organisms) ; Studies ; Usage ; Varieties ; Wine ; Wine and wine making ; Wines ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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