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  • 1
    Article
    Article
    TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast
    2013
    ISSN: 1474-9718 
    Details
    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
    DOI: 10.1111/acel.12080
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    Source: Wiley-Blackwell Full Collection 2014
    URL: https://www.ncbi.nlm.nih.gov/pubmed/23551936$$D View this record in MEDLINE/PubMed
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  • 2
    Article
    Article
    Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells
    2012
    ISSN: 0092-8674 
    Details
    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
    DOI: 10.1016/j.cell.2012.09.019
    Source: Backfile Package - All of Back Files EBS [ALLOFBCKF]
    URL: https://www.ncbi.nlm.nih.gov/pubmed/23101633$$D View this record in MEDLINE/PubMed
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  • 3
    Article
    Article
    A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice
    2014
    ISSN: 2041-1723 
    Details
    Language: English
    In: Nature communications, 2014-06-09, Vol.5 (1), p.4091-4091
    Description: DNA double-strand break (DSB) repair is a highly regulated process performed predominantly by non-homologous end joining (NHEJ) or homologous recombination (HR) pathways. How these pathways are coordinated in the context of chromatin is unclear. Here we uncover a role for histone H3K36 modification in regulating DSB repair pathway choice in fission yeast. We find Set2-dependent H3K36 methylation reduces chromatin accessibility, reduces resection and promotes NHEJ, while antagonistic Gcn5-dependent H3K36 acetylation increases chromatin accessibility, increases resection and promotes HR. Accordingly, loss of Set2 increases H3K36Ac, chromatin accessibility and resection, while Gcn5 loss results in the opposite phenotypes following DSB induction. Further, H3K36 modification is cell cycle regulated with Set2-dependent H3K36 methylation peaking in G1 when NHEJ occurs, while Gcn5-dependent H3K36 acetylation peaks in S/G2 when HR prevails. These findings support an H3K36 chromatin switch in regulating DSB repair pathway choice.
    Subject(s): Acetylation ; Acetyltransferases - metabolism ; Chromatin - metabolism ; DNA End-Joining Repair ; DNA Repair ; DNA, Fungal - metabolism ; Histone-Lysine N-Methyltransferase - metabolism ; Histones - metabolism ; Methylation ; Recombinational DNA Repair ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - metabolism
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    DOI: 10.1038/ncomms5091
    Source: Nature Open Access
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    URL: https://www.ncbi.nlm.nih.gov/pubmed/24909977$$D View this record in MEDLINE/PubMed
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  • 4
    Article
    Article
    The GATA Transcription Factor Gaf1 Represses tRNAs, Inhibits Growth, and Extends Chronological Lifespan Downstream of Fission Yeast TORC1
    2020
    ISSN: 2211-1247 
    Details
    Language: English
    In: Cell reports (Cambridge), 2020-03-10, Vol.30 (10), p.3240-3249.e4
    Description: Target of Rapamycin Complex 1 (TORC1) signaling promotes growth and aging. Inhibition of TORC1 leads to reduced protein translation, which promotes longevity. TORC1-dependent post-transcriptional regulation of protein translation has been well studied, while analogous transcriptional regulation is less understood. Here we screen fission yeast mutants for resistance to Torin1, which inhibits TORC1 and cell growth. Cells lacking the GATA factor Gaf1 (gaf1Δ) grow normally even in high doses of Torin1. The gaf1Δ mutation shortens the chronological lifespan of non-dividing cells and diminishes Torin1-mediated longevity. Expression profiling and genome-wide binding experiments show that upon TORC1 inhibition, Gaf1 directly upregulates genes for small-molecule metabolic pathways and indirectly represses genes for protein translation. Surprisingly, Gaf1 binds to and downregulates the tRNA genes, so it also functions as a transcription factor for RNA polymerase III. Thus, Gaf1 controls the transcription of both protein-coding and tRNA genes to inhibit translation and growth downstream of TORC1. [Display omitted] •Cells lacking the GATA transcription factor Gaf1 grow normally after blocking TORC1•Gaf1 is required for the normal chronological lifespan of non-dividing cells•Gaf1 regulates transcription of protein-coding genes and of tRNA genes•Upon TORC1 block, Gaf1 represses tRNAs to inhibit translation and promote longevity TORC1 signaling promotes protein translation and cellular aging. Rodríguez-López et al. show that this role of TORC1 is partly mediated via the transcription factor Gaf1. When TORC1 is blocked, Gaf1 extends the cellular lifespan by inhibiting the transcription not only of protein-coding genes but also of tRNA genes functioning in translation.
    Subject(s): aging ; cell growth ; GATA6 ; Gene Expression Regulation, Fungal - drug effects ; Genes, Fungal ; Mechanistic Target of Rapamycin Complex 1 - metabolism ; Mutation - genetics ; Naphthyridines - pharmacology ; Open Reading Frames - genetics ; Protein Binding - drug effects ; protein translation ; RNA polymerase III ; RNA, Transfer - metabolism ; S. pombe ; Schizosaccharomyces - drug effects ; Schizosaccharomyces - genetics ; Schizosaccharomyces - growth & development ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - metabolism ; TOR ; Trans-Activators - metabolism ; transcription factor ; Transcriptome - genetics ; tRNA ; vacuole
    ISSN: 2211-1247
    E-ISSN: 2211-1247
    DOI: 10.1016/j.celrep.2020.02.058
    Source: Alma/SFX Local Collection
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    URL: https://www.ncbi.nlm.nih.gov/pubmed/32160533$$D View this record in MEDLINE/PubMed
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  • 5
    Article
    Article
    Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast
    2014
    ISSN: 1744-4292 
    Details
    Language: English
    In: Molecular systems biology, 2014-11, Vol.10 (11), p.764-n/a
    Description: Our current understanding of how natural genetic variation affects gene expression beyond well‐annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci (eQTLs) has the potential to close this gap. Here, we generated the first recombinant strain library for fission yeast and conducted an RNA‐seq‐based QTL study of the coding, non‐coding, and antisense transcriptomes. We show that the frequency of distal effects (trans‐eQTLs) greatly exceeds the number of local effects (cis‐eQTLs) and that non‐coding RNAs are as likely to be affected by eQTLs as protein‐coding RNAs. We identified a genetic variation of swc5 that modifies the levels of 871 RNAs, with effects on both sense and antisense transcription, and show that this effect most likely goes through a compromised deposition of the histone variant H2A.Z. The strains, methods, and datasets generated here provide a rich resource for future studies. Synopsis A large‐scale eQTL study of coding, non‐coding, and antisense transcripts, performed using a recombinant fission yeast strain library, reveals the prevalence of trans‐eQTLs and identifies a variant affecting thousands of expression traits, presumably via epigenetic modification. A fission yeast strain library suitable for quantitative trait locus (QTL) analyses is generated and characterized. A QTL analysis of sense, antisense, coding, and non‐coding expression as well as growth traits is performed. Non‐coding genes are subject to eQTL control as much as coding genes. Trans‐eQTLs are far more abundant than cis‐eQTLs. A swc5 variant impacting thousands of sense and antisense traits, presumably through epigenetic modification (H2A.Z occupancy), is identified. A large‐scale eQTL study of coding, non‐coding, and antisense transcripts, performed using a recombinant fission yeast strain library, reveals the prevalence of trans‐eQTLs and identifies a variant affecting thousands of expression traits, presumably via epigenetic modification.
    Subject(s): Antisense RNA ; antisense transcription ; Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; Design ; Epigenesis, Genetic ; Experiments ; Fission ; Gene expression ; Gene Expression Regulation, Fungal ; Gene mapping ; Gene sequencing ; Genetic diversity ; Genetic Variation ; Genomes ; histone variant ; Laboratories ; non-coding RNA ; Ontology ; Power ; QTL ; Quantitative Trait Loci ; Ribonucleic acid ; RNA ; RNA, Fungal - metabolism ; Schizosaccharomyces - genetics ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Studies ; Transcription ; Transcriptome ; Variation ; Yeast ; Yeasts
    ISSN: 1744-4292
    E-ISSN: 1744-4292
    DOI: 10.15252/msb.20145123
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    Source: Wiley-Blackwell Full Collection 2014
    URL: https://www.ncbi.nlm.nih.gov/pubmed/25432776$$D View this record in MEDLINE/PubMed
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  • 6
    Article
    Article
    S. pombe btn1, the orthologue of the Batten disease gene CLN3, is required for vacuole protein sorting of Cpy1p and Golgi exit of Vps10p
    2009
    ISSN: 0021-9533 
    Details
    Language: English
    In: Journal of cell science, 2009-04-15, Vol.122 (Pt 8), p.1163-1173
    Description: Batten disease is characterised by lysosomal dysfunction. The most common type of the disease is caused by mutations in the membrane protein CLN3, whose function is unknown. We show that the fission yeast orthologue Btn1p, previously implicated in vacuole function, is required for correct sorting of the vacuole hydrolase carboxypeptidase Y (Cpy1p). This is, in part, due to a defect in trafficking of Vps10p, the sorting receptor for Cpy1p, from the Golgi to the trans-Golgi network in btn1Delta cells. Our data also implicate btn1 in other Vps10-independent Cpy1-sorting pathways. Furthermore, btn1 affects the number, intracellular location and structure of Golgi compartments. We show that the prevacuole location of Btn1p is at the Golgi, because Btn1p colocalises predominantly with the Golgi marker Gms1p in compartments that are sensitive to Brefeldin A. Btn1p function might be linked to that of Vps34p, a phosphatidylinositol 3-kinase, because Btn1p acts as a multicopy suppressor of the severe Cpy1p vacuole protein-sorting defect of vps34Delta cells. Together, these results indicate an important role for Btn1p in the Golgi complex, which affects Golgi homeostasis and vacuole protein sorting. We propose a similar role for CLN3 in mammalian cells.
    Subject(s): Batten ; btn1 ; Carboxypeptidase Y ; Cathepsin A - genetics ; Cathepsin A - metabolism ; CLN3 ; Golgi ; Golgi Apparatus - metabolism ; Humans ; Membrane Glycoproteins - genetics ; Membrane Glycoproteins - metabolism ; Membrane Proteins - genetics ; Membrane Proteins - metabolism ; Molecular Chaperones - genetics ; Molecular Chaperones - metabolism ; Mutation ; Neurodegeneration ; Neuronal ceroid lipofuscinosis ; Neuronal Ceroid-Lipofuscinoses - genetics ; Neuronal Ceroid-Lipofuscinoses - metabolism ; Phosphatidylinositol 3-Kinases - metabolism ; Protein Transport ; S. pombe ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Time Factors ; Vacuole ; Vacuoles - metabolism ; Vesicular Transport Proteins - genetics ; Vesicular Transport Proteins - metabolism ; vps10
    ISSN: 0021-9533
    E-ISSN: 1477-9137
    DOI: 10.1242/jcs.038323
    Source: HighWire Press (Free Journals)
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
    Source: Company of Biologists
    URL: https://www.ncbi.nlm.nih.gov/pubmed/19299465$$D View this record in MEDLINE/PubMed
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  • 7
    Article
    Article
    LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq
    2014
    ISSN: 1088-9051 
    Details
    Language: English
    In: Genome research, 2014-07, Vol.24 (7), p.1169-1179
    Description: Both canonical and alternative splicing of RNAs are governed by intronic sequence elements and produce transient lariat structures fastened by branch points within introns. To map precisely the location of branch points on a genomic scale, we developed LaSSO (Lariat Sequence Site Origin), a data-driven algorithm which utilizes RNA-seq data. Using fission yeast cells lacking the debranching enzyme Dbr1, LaSSO not only accurately identified canonical splicing events, but also pinpointed novel, but rare, exon-skipping events, which may reflect aberrantly spliced transcripts. Compromised intron turnover perturbed gene regulation at multiple levels, including splicing and protein translation. Notably, Dbr1 function was also critical for the expression of mitochondrial genes and for the processing of self-spliced mitochondrial introns. LaSSO showed better sensitivity and accuracy than algorithms used for computational branch-point prediction or for empirical branch-point determination. Even when applied to a human data set acquired in the presence of debranching activity, LaSSO identified both canonical and exon-skipping branch points. LaSSO thus provides an effective approach for defining high-resolution maps of branch-site sequences and intronic elements on a genomic scale. LaSSO should be useful to validate introns and uncover branch-point sequences in any eukaryote, and it could be integrated into RNA-seq pipelines.
    Subject(s): Algorithms ; Analysis ; Base Sequence ; Cartography ; Chromosome Mapping ; Computational Biology - methods ; Databases, Nucleic Acid ; Exons ; Gene Deletion ; Gene expression ; Gene Expression Profiling ; Genomics - methods ; High-Throughput Nucleotide Sequencing ; Humans ; Introns ; Method ; Methods ; Nucleotide Motifs ; Position-Specific Scoring Matrices ; Regulatory Sequences, Nucleic Acid ; RNA ; RNA Precursors - genetics ; RNA Splicing ; RNA, Fungal - genetics ; Schizosaccharomyces - genetics ; Schizosaccharomyces pombe ; Sequences (Mathematics) ; Transcription, Genetic ; Transcriptome ; Usage
    ISSN: 1088-9051
    E-ISSN: 1549-5469
    DOI: 10.1101/gr.166819.113
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: Cold Spring Harbor Laboratory Press
    Source: PubMed Central
    Source: Alma/SFX Local Collection
    URL: https://www.ncbi.nlm.nih.gov/pubmed/24709818$$D View this record in MEDLINE/PubMed
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  • 8
    Article
    Article
    Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organisation
    2016
    ISSN: 1469-221X 
    Details
    Language: English
    In: EMBO reports, 2016-01, Vol.17 (1), p.79-93
    Description: Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA‐ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis‐positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re‐establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis‐segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome‐wide. Synopsis Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function. Loss of Abo1 results in a global reduction of histone levels. Nucleosome organisation at gene sequences is perturbed in the absence of Abo1. Abo1 co‐purifies with FACT and suppresses cryptic intragenic transcription. Abo1 function is required for silent centromeric heterochromatin and accurate chromosome segregation. Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function.
    Subject(s): Abo1 ; Adenosine Triphosphatases - chemistry ; Adenosine Triphosphatases - genetics ; Adenosine Triphosphatases - metabolism ; bromodomain AAA-ATPases ; Chromatin ; Chromatin - genetics ; Chromatin - metabolism ; Chromatin Assembly and Disassembly ; Chromatin, Epigenetics, Genomics & Functional Genomics ; Chromosomal Proteins, Non-Histone - metabolism ; Chromosome Segregation ; DNA, Intergenic ; Gene Silencing ; Genes ; Genomes ; Histone Chaperones - genetics ; Histone Chaperones - metabolism ; Histones - genetics ; Histones - metabolism ; nucleosome mapping ; Nucleosomes - genetics ; Nucleosomes - metabolism ; Promoter Regions, Genetic ; RNA Polymerase II - genetics ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - chemistry ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Transcription Factors - metabolism ; Transcription, Genetic
    ISSN: 1469-221X
    E-ISSN: 1469-3178
    DOI: 10.15252/embr.201540476
    Source: HighWire Press (Free Journals)
    Source: Wiley Online Library All Journals
    Source: PubMed Central
    Source: Get It Now
    URL: https://www.ncbi.nlm.nih.gov/pubmed/26582768$$D View this record in MEDLINE/PubMed
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  • 9
    Article
    Article
    Cuf2 is a novel meiosis-specific regulatory factor of meiosis maturation
    2012
    ISSN: 1932-6203 
    Details
    Language: English
    In: PloS one, 2012, Vol.7 (4), p.e36338
    Description: Meiosis is the specialized form of the cell cycle by which diploid cells produce the haploid gametes required for sexual reproduction. Initiation and progression through meiosis requires that the expression of the meiotic genes is precisely controlled so as to provide the correct gene products at the correct times. During meiosis, four temporal gene clusters are either induced or repressed by a cascade of transcription factors. In this report a novel copper-fist-type regulator, Cuf2, is shown to be expressed exclusively during meiosis. The expression profile of the cuf2(+) mRNA revealed that it was induced during middle-phase meiosis. Both cuf2(+) mRNA and protein levels are unregulated by copper addition or starvation. The transcription of cuf2(+) required the presence of a functional mei4(+) gene encoding a key transcription factor that activates the expression of numerous middle meiotic genes. Microscopic analyses of cells expressing a functional Cuf2-GFP protein revealed that Cuf2 co-localized with both homologous chromosomes and sister chromatids during the meiotic divisions. Cells lacking Cuf2 showed an elevated and sustained expression of several of the middle meiotic genes that persisted even during late meiosis. Moreover, cells carrying disrupted cuf2Δ/cuf2Δ alleles displayed an abnormal morphology of the forespore membranes and a dramatic reduction of spore viability. Collectively, the results revealed that Cuf2 functions in the timely repression of the middle-phase genes during meiotic differentiation.
    Subject(s): Amino Acid Sequence ; Anaphase ; Biology ; Cell cycle ; Cell Cycle Proteins - chemistry ; Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; Cell division ; Chromatids ; Chromosomes ; Chromosomes, Fungal - genetics ; Copper ; Deoxyribonucleic acid ; DNA ; DNA binding proteins ; DNA polymerase ; Gametes ; Gene clusters ; Gene Deletion ; Gene expression ; Gene Expression Regulation, Fungal ; Gene silencing ; Genes ; Genetic recombination ; Genetic research ; Genetic transcription ; Genomes ; Genomics ; Green fluorescent protein ; Homology ; Intracellular Space - metabolism ; Iron ; Kinases ; Meiosis ; Membranes ; Metaphase ; Molecular Sequence Data ; Nitrogen ; Protein Transport ; Proteins ; Reproduction (biology) ; RNA ; Schizosaccharomyces - cytology ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - chemistry ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Sexual reproduction ; Sister chromatids ; Spores, Fungal - genetics ; Spores, Fungal - metabolism ; Starvation ; Transcription factors ; Viability ; Yeast
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    DOI: 10.1371/journal.pone.0036338
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
    URL: https://www.ncbi.nlm.nih.gov/pubmed/22558440$$D View this record in MEDLINE/PubMed
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  • 10
    Article
    Article
    Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
    2015
    ISSN: 1088-9051 
    Details
    Language: English
    In: Genome research, 2015-06, Vol.25 (6), p.884-896
    Description: Exon skipping is considered a principal mechanism by which eukaryotic cells expand their transcriptome and proteome repertoires, creating different splice variants with distinct cellular functions. Here we analyze RNA-seq data from 116 transcriptomes in fission yeast (Schizosaccharomyces pombe), covering multiple physiological conditions as well as transcriptional and RNA processing mutants. We applied brute-force algorithms to detect all possible exon-skipping events, which were widespread but rare compared to normal splicing events. Exon-skipping events increased in cells deficient for the nuclear exosome or the 5'-3' exonuclease Dhp1, and also at late stages of meiotic differentiation when nuclear-exosome transcripts decreased. The pervasive exon-skipping transcripts were stochastic, did not increase in specific physiological conditions, and were mostly present at less than one copy per cell, even in the absence of nuclear RNA surveillance and during late meiosis. These exon-skipping transcripts are therefore unlikely to be functional and may reflect splicing errors that are actively removed by nuclear RNA surveillance. The average splicing rate by exon skipping was ∼ 0.24% in wild type and ∼ 1.75% in nuclear exonuclease mutants. We also detected approximately 250 circular RNAs derived from single or multiple exons. These circular RNAs were rare and stochastic, although a few became stabilized during quiescence and in splicing mutants. Using an exhaustive search algorithm, we also uncovered thousands of previously unknown splice sites, indicating pervasive splicing; yet most of these splicing variants were cryptic and increased in nuclear degradation mutants. This study highlights widespread but low frequency alternative or aberrant splicing events that are targeted by nuclear RNA surveillance.
    Subject(s): Alternative Splicing ; Exon (Molecular genetics) ; Exons ; Exoribonucleases - genetics ; Exoribonucleases - metabolism ; Genetic aspects ; Genome, Fungal ; Meiosis ; Physiological aspects ; Research ; RNA - genetics ; RNA - metabolism ; RNA sequencing ; RNA, Circular ; RNA, Nuclear - genetics ; RNA, Nuclear - metabolism ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Sequence Alignment ; Sequence Analysis, RNA ; Transcriptome ; Usage ; Yeast fungi
    ISSN: 1088-9051
    E-ISSN: 1549-5469
    DOI: 10.1101/gr.185371.114
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: Cold Spring Harbor Laboratory Press
    Source: PubMed Central
    Source: Alma/SFX Local Collection
    URL: https://www.ncbi.nlm.nih.gov/pubmed/25883323$$D View this record in MEDLINE/PubMed
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