1
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Andric V, Rougemaille M. Long Non-Coding RNAs in the Control of Gametogenesis: Lessons from Fission Yeast. Noncoding RNA 2021; 7:ncrna7020034. [PMID: 34208016 PMCID: PMC8293462 DOI: 10.3390/ncrna7020034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to cell fate decisions by modulating genome expression and stability. In the fission yeast Schizosaccharomyces pombe, the transition from mitosis to meiosis results in a marked remodeling of gene expression profiles, which ultimately ensures gamete production and inheritance of genetic information to the offspring. This key developmental process involves a set of dedicated lncRNAs that shape cell cycle-dependent transcriptomes through a variety of mechanisms, including epigenetic modifications and the modulation of transcription, post-transcriptional and post-translational regulations, and that contribute to meiosis-specific chromosomal events. In this review, we summarize the biology of these lncRNAs, from their identification to mechanism of action, and discuss their regulatory role in the control of gametogenesis.
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Affiliation(s)
- Vedrana Andric
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Institute Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75005 Paris, France;
| | - Mathieu Rougemaille
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Correspondence:
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2
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CDK Regulation of Meiosis: Lessons from S. cerevisiae and S. pombe. Genes (Basel) 2020; 11:genes11070723. [PMID: 32610611 PMCID: PMC7397238 DOI: 10.3390/genes11070723] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic progression requires precise orchestration, such that one round of DNA replication is followed by two meiotic divisions. The order and timing of meiotic events is controlled through the modulation of the phosphorylation state of proteins. Key components of this phospho-regulatory system include cyclin-dependent kinase (CDK) and its cyclin regulatory subunits. Over the past two decades, studies in budding and fission yeast have greatly informed our understanding of the role of CDK in meiotic regulation. In this review, we provide an overview of how CDK controls meiotic events in both budding and fission yeast. We discuss mechanisms of CDK regulation through post-translational modifications and changes in the levels of cyclins. Finally, we highlight the similarities and differences in CDK regulation between the two yeast species. Since CDK and many meiotic regulators are highly conserved, the findings in budding and fission yeasts have revealed conserved mechanisms of meiotic regulation among eukaryotes.
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3
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Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
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Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
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4
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Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum. mBio 2018; 9:mBio.01292-18. [PMID: 30108170 PMCID: PMC6094484 DOI: 10.1128/mbio.01292-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Long noncoding RNA (lncRNA) plays important roles in sexual development in eukaryotes. In filamentous fungi, however, little is known about the expression and roles of lncRNAs during fruiting body formation. By profiling developmental transcriptomes during the life cycle of the plant-pathogenic fungus Fusarium graminearum, we identified 547 lncRNAs whose expression was highly dynamic, with about 40% peaking at the meiotic stage. Many lncRNAs were found to be antisense to mRNAs, forming 300 sense-antisense pairs. Although small RNAs were produced from these overlapping loci, antisense lncRNAs appeared not to be involved in gene silencing pathways. Genome-wide analysis of small RNA clusters identified many silenced loci at the meiotic stage. However, we found transcriptionally active small RNA clusters, many of which were associated with lncRNAs. Also, we observed that many antisense lncRNAs and their respective sense transcripts were induced in parallel as the fruiting bodies matured. The nonsense-mediated decay (NMD) pathway is known to determine the fates of lncRNAs as well as mRNAs. Thus, we analyzed mutants defective in NMD and identified a subset of lncRNAs that were induced during sexual development but suppressed by NMD during vegetative growth. These results highlight the developmental stage-specific nature and functional potential of lncRNA expression in shaping the fungal fruiting bodies and provide fundamental resources for studying sexual stage-induced lncRNAs. Fusarium graminearum is the causal agent of the head blight on our major staple crops, wheat and corn. The fruiting body formation on the host plants is indispensable for the disease cycle and epidemics. Long noncoding RNA (lncRNA) molecules are emerging as key regulatory components for sexual development in animals and plants. To date, however, there is a paucity of information on the roles of lncRNAs in fungal fruiting body formation. Here we characterized hundreds of lncRNAs that exhibited developmental stage-specific expression patterns during fruiting body formation. Also, we discovered that many lncRNAs were induced in parallel with their overlapping transcripts on the opposite DNA strand during sexual development. Finally, we found a subset of lncRNAs that were regulated by an RNA surveillance system during vegetative growth. This research provides fundamental genomic resources that will spur further investigations on lncRNAs that may play important roles in shaping fungal fruiting bodies.
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5
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Watts BR, Wittmann S, Wery M, Gautier C, Kus K, Birot A, Heo DH, Kilchert C, Morillon A, Vasiljeva L. Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Nucleic Acids Res 2018; 46:5426-5440. [PMID: 29618061 PMCID: PMC6009587 DOI: 10.1093/nar/gky232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022] Open
Abstract
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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Affiliation(s)
- Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Institut für Biochemie, Heinrich-Buff-Ring 17, 35392 Gießen, Germany
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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6
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Zhou S, Sternglanz R, Neiman AM. Developmentally regulated internal transcription initiation during meiosis in budding yeast. PLoS One 2017; 12:e0188001. [PMID: 29136644 PMCID: PMC5685637 DOI: 10.1371/journal.pone.0188001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Sporulation of budding yeast is a developmental process in which cells undergo meiosis to generate stress-resistant progeny. The dynamic nature of the budding yeast meiotic transcriptome has been well established by a number of genome-wide studies. Here we develop an analysis pipeline to systematically identify novel transcription start sites that reside internal to a gene. Application of this pipeline to data from a synchronized meiotic time course reveals over 40 genes that display specific internal initiations in mid-sporulation. Consistent with the time of induction, motif analysis on upstream sequences of these internal transcription start sites reveals a significant enrichment for the binding site of Ndt80, the transcriptional activator of middle sporulation genes. Further examination of one gene, MRK1, demonstrates the Ndt80 binding site is necessary for internal initiation and results in the expression of an N-terminally truncated protein isoform. When the MRK1 paralog RIM11 is downregulated, the MRK1 internal transcript promotes efficient sporulation, indicating functional significance of the internal initiation. Our findings suggest internal transcriptional initiation to be a dynamic, regulated process with potential functional impacts on development.
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Affiliation(s)
- Sai Zhou
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, United States of America
| | - Rolf Sternglanz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
| | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America
- * E-mail:
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7
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Mostovoy Y, Thiemicke A, Hsu TY, Brem RB. The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. Genome Biol Evol 2016; 8:1748-61. [PMID: 27190003 PMCID: PMC4943177 DOI: 10.1093/gbe/evw104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genes encoded close to one another on the chromosome are often coexpressed, by a mechanism and regulatory logic that remain poorly understood. We surveyed the yeast genome for tandem gene pairs oriented tail-to-head at which expression antisense to the upstream gene was conserved across species. The intergenic region at most such tandem pairs is a bidirectional promoter, shared by the downstream gene mRNA and the upstream antisense transcript. Genomic analyses of these intergenic loci revealed distinctive patterns of transcription factor regulation. Mutation of a given transcription factor verified its role as a regulator in trans of tandem gene pair loci, including the proximally initiating upstream antisense transcript and downstream mRNA and the distally initiating upstream mRNA. To investigate cis-regulatory activity at such a locus, we focused on the stress-induced NAD(P)H dehydratase YKL151C and its downstream neighbor, the metabolic enzyme GPM1. Previous work has implicated the region between these genes in regulation of GPM1 expression; our mutation experiments established its function in rich medium as a repressor in cis of the distally initiating YKL151C sense RNA, and an activator of the proximally initiating YKL151C antisense RNA. Wild-type expression of all three transcripts required the transcription factor Gcr2. Thus, at this locus, the intergenic region serves as a focal point of regulatory input, driving antisense expression and mediating the coordinated regulation of YKL151C and GPM1. Together, our findings implicate transcription factors in the joint control of neighboring genes specialized to opposing conditions and the antisense transcripts expressed between them.
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Affiliation(s)
- Yulia Mostovoy
- Department of Molecular and Cell Biology, University of California, Berkeley, California Present address: Cardiovascular Research Institute, University of California, San Francisco, CA
| | - Alexander Thiemicke
- Department of Molecular and Cell Biology, University of California, Berkeley, California Program in Molecular Medicine, Friedrich-Schiller-Universität, Jena, Germany Present address: Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Tiffany Y Hsu
- Department of Molecular and Cell Biology, University of California, Berkeley, California Present address: Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA
| | - Rachel B Brem
- Department of Molecular and Cell Biology, University of California, Berkeley, California Present address: Buck Institute for Research on Aging, Novato, CA
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8
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Cuf2 Is a Transcriptional Co-Regulator that Interacts with Mei4 for Timely Expression of Middle-Phase Meiotic Genes. PLoS One 2016; 11:e0151914. [PMID: 26986212 PMCID: PMC4795683 DOI: 10.1371/journal.pone.0151914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/07/2016] [Indexed: 11/19/2022] Open
Abstract
The Schizosaccharomyces pombe cuf2+ gene encodes a nuclear regulator that is required for timely activation and repression of several middle-phase genes during meiotic differentiation. In this study, we sought to gain insight into the mechanism by which Cuf2 regulates meiotic gene expression. Using a chromatin immunoprecipitation approach, we demonstrate that Cuf2 is specifically associated with promoters of both activated and repressed target genes, in a time-dependent manner. In case of the fzr1+ gene whose transcription is positively affected by Cuf2, promoter occupancy by Cuf2 results in a concomitant increased association of RNA polymerase II along its coding region. In marked contrast, association of RNA polymerase II with chromatin decreases when Cuf2 negatively regulates target gene expression such as wtf13+. Although Cuf2 operates through a transcriptional mechanism, it is unable to perform its function in the absence of the Mei4 transcription factor, which is a member of the conserved forkhead protein family. Using coimmunoprecipitation experiments, results showed that Cuf2 is a binding partner of Mei4. Bimolecular fluorescence complementation experiments brought further evidence that an association between Cuf2 and Mei4 occurs in the nucleus. Analysis of fzr1+ promoter regions revealed that two FLEX-like elements, which are bound by the transcription factor Mei4, are required for chromatin occupancy by Cuf2. Together, results reported here revealed that Cuf2 and Mei4 co-regulate the timely expression of middle-phase genes during meiosis.
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9
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Alves-Rodrigues I, Ferreira PG, Moldón A, Vivancos AP, Hidalgo E, Guigó R, Ayté J. Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program. Cell Rep 2016; 14:885-895. [PMID: 26804917 DOI: 10.1016/j.celrep.2015.12.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/13/2015] [Accepted: 12/15/2015] [Indexed: 01/06/2023] Open
Abstract
Meiosis is a differentiated program of the cell cycle that is characterized by high levels of recombination followed by two nuclear divisions. In fission yeast, the genetic program during meiosis is regulated at multiple levels, including transcription, mRNA stabilization, and splicing. Mei4 is a forkhead transcription factor that controls the expression of mid-meiotic genes. Here, we describe that Fkh2, another forkhead transcription factor that is essential for mitotic cell-cycle progression, also plays a pivotal role in the control of meiosis. Fkh2 binding preexists in most Mei4-dependent genes, inhibiting their expression. During meiosis, Fkh2 is phosphorylated in a CDK/Cig2-dependent manner, decreasing its affinity for DNA, which creates a window of opportunity for Mei4 binding to its target genes. We propose that Fkh2 serves as a placeholder until the later appearance of Mei4 with a higher affinity for DNA that induces the expression of a subset of meiotic genes.
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Affiliation(s)
- Isabel Alves-Rodrigues
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Pedro G Ferreira
- Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Alberto Moldón
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Ana P Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Elena Hidalgo
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Roderic Guigó
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain; Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - José Ayté
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
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10
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Normant V, Beaudoin J, Labbé S. An antisense RNA-mediated mechanism eliminates a meiosis-specific copper-regulated transcript in mitotic cells. J Biol Chem 2015; 290:22622-37. [PMID: 26229103 DOI: 10.1074/jbc.m115.674556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
Sense and antisense transcripts produced from convergent gene pairs could interfere with the expression of either partner gene. In Schizosaccharomyces pombe, we found that the iss1(+) gene produces two transcript isoforms, including a long antisense mRNA that is complementary to the meiotic cum1(+) sense transcript, inhibiting cum1(+) expression in vegetative cells. Inhibition of cum1(+) transcription was not at the level of its initiation because fusion of the cum1(+) promoter to the lacZ gene showed that activation of the reporter gene occurs in response to low copper conditions. Further analysis showed that the transcription factor Cuf1 and conserved copper-signaling elements (CuSEs) are required for induction of cum1(+)-lacZ transcription under copper deficiency. Insertion of a multipartite polyadenylation signal immediately downstream of iss1(+) led to the exclusive production of a shorter iss1(+) mRNA isoform, thereby allowing accumulation of cum1(+) sense mRNA in copper-limited vegetative cells. This finding suggested that the long iss1(+) antisense mRNA could pair with cum1(+) sense mRNA, thereby producing double-stranded RNA molecules that could induce RNAi. We consistently found that mutant strains for RNAi (dcr1Δ, ago1Δ, rdp1Δ, and clr4Δ) are defective in selectively eliminating cum1(+) sense transcript in the G1 phase of the cell cycle. Taken together, these results describe the first example of a copper-regulated meiotic gene repressed by an antisense transcription mechanism in vegetative cells.
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Affiliation(s)
- Vincent Normant
- From the Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Jude Beaudoin
- From the Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Simon Labbé
- From the Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
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11
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Oda A, Takemata N, Hirata Y, Miyoshi T, Suzuki Y, Sugano S, Ohta K. Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation. Genes Cells 2015; 20:392-407. [DOI: 10.1111/gtc.12229] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Arisa Oda
- Department of Biophysics and Biochemistry Graduate School of Science The University of Tokyo Hongo Tokyo 113‐0033 Japan
| | - Naomichi Takemata
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Meguro‐ku Tokyo 153‐8902 Japan
| | - Yoshito Hirata
- Institute of Industrial Science The University of Tokyo Meguro‐ku Tokyo 153‐8505 Japan
| | - Tomoichiro Miyoshi
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Meguro‐ku Tokyo 153‐8902 Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Chiba 277‐8561 Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Chiba 277‐8561 Japan
| | - Kunihiro Ohta
- Department of Biophysics and Biochemistry Graduate School of Science The University of Tokyo Hongo Tokyo 113‐0033 Japan
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Meguro‐ku Tokyo 153‐8902 Japan
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12
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Clément-Ziza M, Marsellach FX, Codlin S, Papadakis MA, Reinhardt S, Rodríguez-López M, Martin S, Marguerat S, Schmidt A, Lee E, Workman CT, Bähler J, Beyer A. Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast. Mol Syst Biol 2014; 10:764. [PMID: 25432776 PMCID: PMC4299605 DOI: 10.15252/msb.20145123] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Mathieu Clément-Ziza
- Biotechnology Centre, Technische Universität Dresden, Dresden, Germany Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Francesc X Marsellach
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Sandra Codlin
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Manos A Papadakis
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Susanne Reinhardt
- Biotechnology Centre, Technische Universität Dresden, Dresden, Germany
| | - María Rodríguez-López
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Stuart Martin
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Samuel Marguerat
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | | | - Eunhye Lee
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London, UK
| | - Andreas Beyer
- Biotechnology Centre, Technische Universität Dresden, Dresden, Germany Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
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13
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Fowler KR, Sasaki M, Milman N, Keeney S, Smith GR. Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome. Genome Res 2014; 24:1650-64. [PMID: 25024163 PMCID: PMC4199369 DOI: 10.1101/gr.172122.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fission yeast Rec12 (Spo11 homolog) initiates meiotic recombination by forming developmentally programmed DNA double-strand breaks (DSBs). DSB distributions influence patterns of heredity and genome evolution, but the basis of the highly nonrandom choice of Rec12 cleavage sites is poorly understood, largely because available maps are of relatively low resolution and sensitivity. Here, we determined DSBs genome-wide at near-nucleotide resolution by sequencing the oligonucleotides attached to Rec12 following DNA cleavage. The single oligonucleotide size class allowed us to deeply sample all break events. We find strong evidence across the genome for differential DSB repair accounting for crossover invariance (constant cM/kb in spite of DSB hotspots). Surprisingly, about half of all crossovers occur in regions where DSBs occur at low frequency and are widely dispersed in location from cell to cell. These previously undetected, low-level DSBs thus play an outsized and crucial role in meiosis. We further find that the influence of underlying nucleotide sequence and chromosomal architecture differs in multiple ways from that in budding yeast. DSBs are not strongly restricted to nucleosome-depleted regions, as they are in budding yeast, but are nevertheless spatially influenced by chromatin structure. Our analyses demonstrate that evolutionarily fluid factors contribute to crossover initiation and regulation.
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Affiliation(s)
- Kyle R Fowler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Mariko Sasaki
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10065, USA
| | - Neta Milman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10065, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
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14
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A novel histone deacetylase complex in the control of transcription and genome stability. Mol Cell Biol 2014; 34:3500-14. [PMID: 25002536 DOI: 10.1128/mcb.00519-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The acetylation state of histones, controlled by histone acetyltransferases (HATs) and deacetylases (HDACs), profoundly affects DNA transcription and repair by modulating chromatin accessibility to the cellular machinery. The Schizosaccharomyces pombe HDAC Clr6 (human HDAC1) binds to different sets of proteins that define functionally distinct complexes: I, I', and II. Here, we determine the composition, architecture, and functions of a new Clr6 HDAC complex, I'', delineated by the novel proteins Nts1, Mug165, and Png3. Deletion of nts1 causes increased sensitivity to genotoxins and deregulated expression of Tf2 elements, long noncoding RNA, and subtelomeric and stress-related genes. Similar, but more pervasive, phenotypes are observed upon Clr6 inactivation, supporting the designation of complex I'' as a mediator of a key subset of Clr6 functions. We also reveal that with the exception of Tf2 elements, the genome-wide loading sites and loci regulated by Clr6 I″ do not correlate. Instead, Nts1 loads at genes that are expressed in midmeiosis, following oxidative stress, or are periodically expressed. Collective data suggest that Clr6 I'' has (i) indirect effects on gene expression, conceivably by mediating higher-order chromatin organization of subtelomeres and Tf2 elements, and (ii) direct effects on the transcription of specific genes in response to certain cellular or environmental stimuli.
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15
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Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CRM, Miller CJ. A global non-coding RNA system modulates fission yeast protein levels in response to stress. Nat Commun 2014; 5:3947. [PMID: 24853205 PMCID: PMC4050258 DOI: 10.1038/ncomms4947] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/25/2014] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are frequent and prevalent across the taxa. Although individual non-coding loci have been assigned a function, most are uncharacterized. Their global biological significance is unproven and remains controversial. Here we investigate the role played by ncRNAs in the stress response of Schizosaccharomyces pombe. We integrate global proteomics and RNA sequencing data to identify a systematic programme in which elevated antisense RNA arising both from ncRNAs and from 3'-overlapping convergent gene pairs is directly associated with substantial reductions in protein levels throughout the genome. We describe an extensive array of ncRNAs with trans associations that have the potential to influence multiple pathways. Deletion of one such locus reduces levels of atf1, a transcription factor downstream of the stress-activated mitogen-activated protein kinase (MAPK) pathway, and alters sensitivity to oxidative stress. These non-coding transcripts therefore regulate specific stress responses, adding unanticipated information-processing capacity to the MAPK signalling system.
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Affiliation(s)
- Hui Sun Leong
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
- These authors contributed equally to this work
| | - Keren Dawson
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
- These authors contributed equally to this work
| | - Chris Wirth
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
| | - Yaoyong Li
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
| | - Yvonne Connolly
- Biological Mass Spectrometry Facility, Cancer Research UK
Manchester Institute, University of Manchester, Wilmslow
Road, Manchester
M20 4BX, UK
| | - Duncan L. Smith
- Biological Mass Spectrometry Facility, Cancer Research UK
Manchester Institute, University of Manchester, Wilmslow
Road, Manchester
M20 4BX, UK
| | - Caroline R. M. Wilkinson
- Cell Regulation Group, Cancer Research UK Manchester Institute,
University of Manchester, Wilmslow Road,
Manchester
M20 4BX, UK
| | - Crispin J. Miller
- Applied Computational Biology and Bioinformatics Group, Cancer
Research UK Manchester Institute, University of Manchester,
Wilmslow Road, Manchester
M20 4BX, UK
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16
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Boopathi P, Subudhi AK, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Chand B, Mugasimangalam RC, Kochar SK, Sirohi P, Kochar DK, Das A. Revealing natural antisense transcripts from Plasmodium vivax isolates: Evidence of genome regulation in complicated malaria. INFECTION GENETICS AND EVOLUTION 2013; 20:428-43. [DOI: 10.1016/j.meegid.2013.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 01/08/2023]
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17
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Li M, Song B, Zhang Q, Liu X, Lin Y, Ou Y, Zhang H, Liu J. A synthetic tuber-specific and cold-induced promoter is applicable in controlling potato cold-induced sweetening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 67:41-7. [PMID: 23542182 DOI: 10.1016/j.plaphy.2013.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/19/2013] [Indexed: 05/03/2023]
Abstract
Cold-induced sweetening (CIS) in potato seriously hinders the potato processing industry. It could be of great value for genetic improvement of potato CIS to have a target gene specifically expressed in cold stored tubers. In this study, we used a synthetic promoter, pCL, in potato transformation to drive an antisense expression of StvacINV1, the acid vacuolar invertase gene from Solanum tuberosum. The measurements of expression and enzyme activity of target gene showed that pCL promoter could efficiently govern target gene to express specifically and remarkably regulate the activity of acid vacuolar invertase in potato tubers at low temperature, furthermore, it had almost no effect in other tissues or the tubers under room temperature. The transgenic tubers showed decrease in reducing sugar content during storage at low temperature and acceptable chip color without significant changes observed in plant morphology and tuberization between the nontransgenic and transgenic lines. This tuber-specific and cold-induced feature could maximally reduce the background expression of the target gene which might bring about potential negative or detrimental effects to plant development. The synthetic promoter confirmed here would be optimal for gene function research in potato tubers in response to low temperature.
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Affiliation(s)
- Meng Li
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China.
| | - Botao Song
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China.
| | - Qiong Zhang
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Xun Liu
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Yuan Lin
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Yongbin Ou
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Huiling Zhang
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China
| | - Jun Liu
- Key Laboratory of Horticulture Plant Biology, Huazhong Agricultural University, National Center for Vegetable Improvement (Central China), Ministry of Education, Wuhan 430070, People's Republic of China.
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18
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Krug LT. Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq. Curr Opin Virol 2013; 3:276-84. [PMID: 23684513 DOI: 10.1016/j.coviro.2013.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/18/2013] [Indexed: 11/16/2022]
Abstract
Technological advances in genome-wide transcript analysis, referred to as the transcriptome, using microarrays and deep RNA sequencing methodologies are rapidly extending our understanding of the genetic content of the gammaherpesviruses (γHVs). These vast transcript analyses continue to uncover the complexity of coding transcripts due to alternative splicing, translation initiation and termination, as well as regulatory RNAs of the γHVs. A full assessment of the transcriptome requires that our analysis be extended to the virion and exosomes of infected cells since viral and host mRNAs, miRNAs, and other noncoding RNAs seem purposefully incorporated to exert function upon delivery to naïve cells. Understanding the regulation, biogenesis and function of the recently discovered transcripts will extend beyond pathogenesis and oncogenic events to offer key insights for basic RNA processes of the cell.
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Affiliation(s)
- Laurie T Krug
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, United States.
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19
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Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing. BMC Genomics 2013; 14:246. [PMID: 23577966 PMCID: PMC3635940 DOI: 10.1186/1471-2164-14-246] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/06/2013] [Indexed: 12/14/2022] Open
Abstract
Background Genome-wide analysis was performed to assess the transcriptional landscape of germinating A. niger conidia using both next generation RNA-sequencing and GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes. Results The transcriptome of dormant conidia was shown to be highly differentiated from that of germinating conidia and major changes in response to environmental shift occurred within the first hour of germination. The breaking of dormancy was associated with increased transcript levels of genes involved in the biosynthesis of proteins, RNA turnover and respiratory metabolism. Increased transcript levels of genes involved in metabolism of nitrate at the onset of germination implies its use as a source of nitrogen. The transcriptome of dormant conidia contained a significant component of antisense transcripts that changed during germination. Conclusion Dormant conidia contained transcripts of genes involved in fermentation, gluconeogenesis and the glyoxylate cycle. The presence of such transcripts in dormant conidia may indicate the generation of energy from non-carbohydrate substrates during starvation-induced conidiation or for maintenance purposes during dormancy. The immediate onset of metabolism of internal storage compounds after the onset of germination, and the presence of transcripts of relevant genes, suggest that conidia are primed for the onset of germination. For some genes, antisense transcription is regulated in the transition from resting conidia to fully active germinants.
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20
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Sugiyama T, Sugioka-Sugiyama R, Hada K, Niwa R. Rhn1, a nuclear protein, is required for suppression of meiotic mRNAs in mitotically dividing fission yeast. PLoS One 2012; 7:e42962. [PMID: 22912768 PMCID: PMC3422304 DOI: 10.1371/journal.pone.0042962] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/16/2012] [Indexed: 12/23/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, many meiotic mRNAs are transcribed during mitosis and meiosis and selectively eliminated in mitotic cells. However, this pathway for mRNA decay, called the determinant of selective removal (DSR)-Mmi1 system, targets only some of the numerous meiotic mRNAs that are transcribed in mitotic cells. Here we describe Rhn1, a nuclear protein involved in meiotic mRNA suppression in vegetative fission yeast. Rhn1 is homologous to budding yeast Rtt103 and localizes to one or a few discrete nuclear dots in growing vegetative cells. Rhn1 colocalizes with a pre-mRNA 3′-end processing factor, Pcf11, and with the 5′–3′ exoribonuclease, Dhp1; moreover, Rhn1 coimmunoprecipitates with Pcf11. Loss of rhn1 results in elevated sensitivity to high temperature, to thiabendazole (TBZ), and to UV. Interestingly, meiotic mRNAs—including moa1+, mcp5+, and mug96+—accumulate in mitotic rhn1Δ cells. Accumulation of meiotic mRNAs also occurs in strains lacking Lsk1, a kinase that phosphorylates serine 2 (Ser-2) in the C-terminal domain (CTD) of RNA polymerase II (Pol II), and in strains lacking Sen1, an ATP-dependent 5′–3′ RNA/DNA helicase: notably, both Lsk1 and Sen1 have been implicated in termination of Pol II-dependent transcription. Furthermore, RNAi knockdown of cids-2, a Caenorhabditis elegans ortholog of rhn1+, leads to elevated expression of a germline-specific gene, pgl-1, in somatic cells. These results indicate that Rhn1 contributes to the suppression of meiotic mRNAs in vegetative fission yeast and that the mechanism by which Rhn1 downregulates germline-specific transcripts may be conserved in unicellular and multicellular organisms.
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Affiliation(s)
- Tomoyasu Sugiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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22
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Potter K, Cremona N, Sunder S, Wise JA. A dominant role for meiosis-specific 3' RNA processing in controlling expression of a fission yeast cyclin gene. RNA (NEW YORK, N.Y.) 2012; 18:1408-1420. [PMID: 22647846 PMCID: PMC3383971 DOI: 10.1261/rna.033423.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/15/2012] [Indexed: 06/01/2023]
Abstract
Meiotic gene regulation provides a rich source of insight into mechanisms of temporal control during development. We previously reported that accumulation of many meiotic mRNAs in fission yeast is governed by changes in 3' RNA processing and elucidated the molecular basis of this regulatory mechanism for an early meiotic gene. Here, we report that cleavage/polyadenylation is also the nexus of negative control for middle meiotic genes. Parallel profiles of splicing and polyadenylation are observed over a meiotic time course for both rem1 and spo4 but not for a constitutive control gene. Nevertheless, polyadenylation of rem1 transcripts is restricted to meiosis by a splicing-independent mechanism. Through systematic sequence substitutions, we identified a negative control region (NCR) located upstream of the rem1 transcription start site and found that it is required to block 3' RNA processing in proliferating cells. Ablation of the NCR relieves inhibition regardless of whether the intron is present, absent, or carries splice site mutations. Consistent with the previous report of a polypeptide encoded by the first exon of rem1, we discovered a second 3' processing site just downstream from the 5' splice site. Polyadenylation within the intron is activated concurrent with the downstream site during meiosis, is controlled by the NCR, and is enhanced when splicing is blocked via 5' junction or branch point mutations. Taken together, these data suggest a novel regulatory mechanism in which a 5' element modulates the dynamic interplay between splicing and polyadenylation.
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Affiliation(s)
- Kristine Potter
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4960, USA
| | - Nicole Cremona
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4960, USA
| | | | - Jo Ann Wise
- Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4960, USA
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Mmi1 RNA surveillance machinery directs RNAi complex RITS to specific meiotic genes in fission yeast. EMBO J 2012; 31:2296-308. [PMID: 22522705 DOI: 10.1038/emboj.2012.105] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 03/29/2012] [Indexed: 12/24/2022] Open
Abstract
RNA interference (RNAi) silences gene expression by acting both at the transcriptional and post-transcriptional levels in a broad range of eukaryotes. In the fission yeast Schizosaccharomyces pombe the RNA-Induced Transcriptional Silencing (RITS) RNAi complex mediates heterochromatin formation at non-coding and repetitive DNA. However, the targeting and role of RITS at other genomic regions, including protein-coding genes, remain unknown. Here we show that RITS localizes to specific meiotic genes and mRNAs. Remarkably, RITS is guided to these meiotic targets by the RNA-binding protein Mmi1 and its associated RNA surveillance machinery that together degrade selective meiotic mRNAs during vegetative growth. Upon sexual differentiation, RITS localization to the meiotic genes and mRNAs is lost. Large-scale identification of Mmi1 RNA targets reveals that RITS subunit Chp1 associates with the vast majority of them. In addition, loss of RNAi affects the effective repression of sexual differentiation mediated by the Mmi1 RNA surveillance machinery. These findings uncover a new mechanism for recruiting RNAi to specific meiotic genes and suggest that RNAi participates in the control of sexual differentiation in fission yeast.
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24
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Chen HM, Neiman AM. A conserved regulatory role for antisense RNA in meiotic gene expression in yeast. Curr Opin Microbiol 2011; 14:655-9. [PMID: 21963111 DOI: 10.1016/j.mib.2011.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 09/11/2011] [Accepted: 09/12/2011] [Indexed: 01/20/2023]
Abstract
A significant fraction of the eukaryotic genome is transcribed into RNAs that do not encode proteins, termed non-coding RNA (ncRNA). One class of ncRNA that is of particular interest is antisense RNAs, which are complementary to protein coding transcripts (mRNAs). In this article, we summarize recent studies using different yeasts that reveal a conserved pattern in which meiotically expressed genes have antisense transcripts in vegetative cells. These antisense transcripts repress the basal transcription of the mRNA during vegetative growth and are diminished as cells enter meiosis. While the mechanism(s) by which these antisense RNAs interfere with production of sense transcripts is not yet understood, the effects appear to be independent of the canonical RNAi machinery.
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Affiliation(s)
- Huei-Mei Chen
- Department of Microbiology and Molecular Genetics, Stony Brook University, Stony Brook, NY 11794-5215, United States
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