1
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Khanduja JS, Joh RI, Perez MM, Paulo JA, Palmieri CM, Zhang J, Gulka AOD, Haas W, Gygi SP, Motamedi M. RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly. Cell 2024; 187:3262-3283.e23. [PMID: 38815580 PMCID: PMC11227895 DOI: 10.1016/j.cell.2024.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024]
Abstract
In eukaryotes, the Suv39 family of proteins tri-methylate lysine 9 of histone H3 (H3K9me) to form constitutive heterochromatin. However, how Suv39 proteins are nucleated at heterochromatin is not fully described. In the fission yeast, current models posit that Argonaute1-associated small RNAs (sRNAs) nucleate the sole H3K9 methyltransferase, Clr4/SUV39H, to centromeres. Here, we show that in the absence of all sRNAs and H3K9me, the Mtl1 and Red1 core (MTREC)/PAXT complex nucleates Clr4/SUV39H at a heterochromatic long noncoding RNA (lncRNA) at which the two H3K9 deacetylases, Sir2 and Clr3, also accumulate by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4/SUV39H from the nucleation center in an sRNA-independent manner, generating a basal H3K9me state. This is acted upon by the RNAi machinery to augment and amplify the Clr4/H3K9me signal at centromeres to establish heterochromatin. Overall, our data reveal that lncRNAs and RNA quality control factors can nucleate heterochromatin and function as epigenetic silencers in eukaryotes.
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Affiliation(s)
- Jasbeer S Khanduja
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Richard I Joh
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Monica M Perez
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christina M Palmieri
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jingyu Zhang
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alex O D Gulka
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Willhelm Haas
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mo Motamedi
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA.
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2
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Garg A, Schwer B, Shuman S. Fission yeast poly(A) polymerase active site mutation Y86D alleviates the rad24Δ asp1-H397A synthetic growth defect and up-regulates mRNAs targeted by MTREC and Mmi1. RNA (NEW YORK, N.Y.) 2023; 29:1738-1753. [PMID: 37586723 PMCID: PMC10578478 DOI: 10.1261/rna.079722.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/30/2023] [Indexed: 08/18/2023]
Abstract
Expression of fission yeast Pho1 acid phosphatase is repressed under phosphate-replete conditions by transcription of an upstream prt lncRNA that interferes with the pho1 mRNA promoter. lncRNA-mediated interference is alleviated by genetic perturbations that elicit precocious lncRNA 3'-processing and transcription termination, such as (i) the inositol pyrophosphate pyrophosphatase-defective asp1-H397A allele, which results in elevated levels of IP8, and (ii) absence of the 14-3-3 protein Rad24. Combining rad24Δ with asp1-H397A causes a severe synthetic growth defect. A forward genetic screen for SRA (Suppressor of Rad24 Asp1-H397A) mutations identified a novel missense mutation (Tyr86Asp) of Pla1, the essential poly(A) polymerase subunit of the fission yeast cleavage and polyadenylation factor (CPF) complex. The pla1-Y86D allele was viable but slow-growing in an otherwise wild-type background. Tyr86 is a conserved active site constituent that contacts the RNA primer 3' nt and the incoming ATP. The Y86D mutation elicits a severe catalytic defect in RNA-primed poly(A) synthesis in vitro and in binding to an RNA primer. Yet, analyses of specific mRNAs indicate that poly(A) tails in pla1-Y86D cells are not different in size than those in wild-type cells, suggesting that other RNA interactors within CPF compensate for the defects of isolated Pla1-Y86D. Transcriptome profiling of pla1-Y86D cells revealed the accumulation of multiple RNAs that are normally rapidly degraded by the nuclear exosome under the direction of the MTREC complex, with which Pla1 associates. We suggest that Pla1-Y86D is deficient in the hyperadenylation of MTREC targets that precedes their decay by the exosome.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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3
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Grewal SIS. The molecular basis of heterochromatin assembly and epigenetic inheritance. Mol Cell 2023; 83:1767-1785. [PMID: 37207657 PMCID: PMC10309086 DOI: 10.1016/j.molcel.2023.04.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023]
Abstract
Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are essential for the establishment of heterochromatin domains, which is initiated by the recruitment of histone-modifying enzymes to nucleation sites. This leads to the deposition of histone H3 lysine-9 methylation (H3K9me), which provides the foundation for building high-concentration territories of heterochromatin proteins and the spread of heterochromatin across extended domains. Moreover, heterochromatin can be epigenetically inherited during cell division in a self-templating manner. This involves a "read-write" mechanism where pre-existing modified histones, such as tri-methylated H3K9 (H3K9me3), support chromatin association of the histone methyltransferase to promote further deposition of H3K9me. Recent studies suggest that a critical density of H3K9me3 and its associated factors is necessary for the propagation of heterochromatin domains across multiple generations. In this review, I discuss the key experiments that have highlighted the importance of modified histones for epigenetic inheritance.
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Affiliation(s)
- Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T. Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 2023; 14:772. [PMID: 36774373 PMCID: PMC9922296 DOI: 10.1038/s41467-023-36402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
The S. pombe orthologue of the human PAXT connection, Mtl1-Red1 Core (MTREC), is an eleven-subunit complex that targets cryptic unstable transcripts (CUTs) to the nuclear RNA exosome for degradation. It encompasses the canonical poly(A) polymerase Pla1, responsible for polyadenylation of nascent RNA transcripts as part of the cleavage and polyadenylation factor (CPF/CPSF). In this study we identify and characterise the interaction between Pla1 and the MTREC complex core component Red1 and analyse the functional relevance of this interaction in vivo. Our crystal structure of the Pla1-Red1 complex shows that a 58-residue fragment in Red1 binds to the RNA recognition motif domain of Pla1 and tethers it to the MTREC complex. Structure-based Pla1-Red1 interaction mutations show that Pla1, as part of MTREC complex, hyper-adenylates CUTs for their efficient degradation. Interestingly, the Red1-Pla1 interaction is also required for the efficient assembly of the fission yeast facultative heterochromatic islands. Together, our data suggest a complex interplay between the RNA surveillance and 3'-end processing machineries.
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Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Anusree Sivadas
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Nikolay Dobrev
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Rippei Hayashi
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Leo Kiss
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Meyerhofstr, 1, D-69117, Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120, Heidelberg, Germany.
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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5
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Martín Caballero L, Capella M, Barrales RR, Dobrev N, van Emden T, Hirano Y, Suma Sreechakram VN, Fischer-Burkart S, Kinugasa Y, Nevers A, Rougemaille M, Sinning I, Fischer T, Hiraoka Y, Braun S. The inner nuclear membrane protein Lem2 coordinates RNA degradation at the nuclear periphery. Nat Struct Mol Biol 2022; 29:910-921. [PMID: 36123402 PMCID: PMC9507967 DOI: 10.1038/s41594-022-00831-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/02/2022] [Indexed: 11/21/2022]
Abstract
Transcriptionally silent chromatin often localizes to the nuclear periphery. However, whether the nuclear envelope (NE) is a site for post-transcriptional gene repression is not well understood. Here we demonstrate that Schizosaccharomycespombe Lem2, an NE protein, regulates nuclear-exosome-mediated RNA degradation. Lem2 deletion causes accumulation of RNA precursors and meiotic transcripts and de-localization of an engineered exosome substrate from the nuclear periphery. Lem2 does not directly bind RNA but instead interacts with the exosome-targeting MTREC complex and its human homolog PAXT to promote RNA recruitment. This pathway acts largely independently of nuclear bodies where exosome factors assemble. Nutrient availability modulates Lem2 regulation of meiotic transcripts, implying that this pathway is environmentally responsive. Our work reveals that multiple spatially distinct degradation pathways exist. Among these, Lem2 coordinates RNA surveillance of meiotic transcripts and non-coding RNAs by recruiting exosome co-factors to the nuclear periphery. The Braun lab shows that the conserved nuclear membrane protein Lem2 interacts with the MTREC complex of the nuclear-exosome pathway to promote recruitment and degradation of ncRNAs and meiotic transcripts at the nuclear periphery in Schizosaccharomycespombe.
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Affiliation(s)
- Lucía Martín Caballero
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Matías Capella
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ramón Ramos Barrales
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Nikolay Dobrev
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Thomas van Emden
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Vishnu N Suma Sreechakram
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sabine Fischer-Burkart
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Regulation for intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Alicia Nevers
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Tamás Fischer
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.,The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sigurd Braun
- BioMedical Center (BMC), Division of Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany. .,International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany. .,Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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6
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Foucher AE, Touat-Todeschini L, Juarez-Martinez AB, Rakitch A, Laroussi H, Karczewski C, Acajjaoui S, Soler-López M, Cusack S, Mackereth CD, Verdel A, Kadlec J. Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex. Nat Commun 2022; 13:4969. [PMID: 36002457 PMCID: PMC9402713 DOI: 10.1038/s41467-022-32542-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
To eliminate specific or aberrant transcripts, eukaryotes use nuclear RNA-targeting complexes that deliver them to the exosome for degradation. S. pombe MTREC, and its human counterpart PAXT, are key players in this mechanism but inner workings of these complexes are not understood in sufficient detail. Here, we present an NMR structure of an MTREC scaffold protein Red1 helix-turn-helix domain bound to the Iss10 N-terminus and show this interaction is required for proper cellular growth and meiotic mRNA degradation. We also report a crystal structure of a Red1-Ars2 complex explaining mutually exclusive interactions of hARS2 with various ED/EGEI/L motif-possessing RNA regulators, including hZFC3H1 of PAXT, hFLASH or hNCBP3. Finally, we show that both Red1 and hZFC3H1 homo-dimerize via their coiled-coil regions indicating that MTREC and PAXT likely function as dimers. Our results, combining structures of three Red1 interfaces with in vivo studies, provide mechanistic insights into conserved features of MTREC/PAXT architecture.
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Affiliation(s)
| | - Leila Touat-Todeschini
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | | | - Auriane Rakitch
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | - Hamida Laroussi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Claire Karczewski
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble, France
| | - Montserrat Soler-López
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), CS 40220, 38043, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Cameron D Mackereth
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Institut Européen de Chimie et Biologie, 33607, Pessac, France.
| | - André Verdel
- Institut for Advanced Biosciences, UMR Inserm U1209/CNRS 5309/University Grenoble Alpes, La Tronche, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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7
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Ohtsuka H, Imada K, Shimasaki T, Aiba H. Sporulation: A response to starvation in the fission yeast Schizosaccharomyces pombe. Microbiologyopen 2022; 11:e1303. [PMID: 35765188 PMCID: PMC9214231 DOI: 10.1002/mbo3.1303] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe employs two main strategies to adapt to the environment and survive when starved for nutrients. The strategies employ sporulation via sexual differentiation and extension of the chronological lifespan. When a cell is exposed to nutrient starvation in the presence of a cell of the opposite sex, the cells undergo fusion through conjugation and sporulation through meiosis. S. pombe spores are highly resistant to diverse stresses and may survive for a very long time. In this minireview, among the various sexual differentiation processes induced by starvation, we focused on and summarized the findings of the molecular mechanisms of spore formation in fission yeast. Furthermore, comparative measurements of the chronological lifespan of stationary phase cells and G0 cells and the survival period of spore cells revealed that the spore cells survived for a long period, indicating the presence of an effective mechanism for survival. Currently, many molecules involved in sporulation and their functions are being discovered; however, our understanding of these is not complete. Further understanding of spores may not only deepen our comprehension of sexual differentiation but may also provide hints for sustaining life.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Kazuki Imada
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka, Japan.,Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
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8
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Shen S, Jian Y, Cai Z, Li F, Lv M, Liu Y, Wu J, Fu C, Shi Y. Structural insights reveal the specific recognition of meiRNA by the Mei2 protein. J Mol Cell Biol 2022; 14:6581319. [PMID: 35512546 PMCID: PMC9486875 DOI: 10.1093/jmcb/mjac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, Mei2, an RNA-binding protein essential for entry into meiosis, regulates meiosis initiation. Mei2 binds to a specific non-coding RNA species, meiRNA, and accumulates at sme2 gene locus, which encodes meiRNA. Previous research has shown that the Mei2 C-terminal RNA recognition motif (RRM3) physically interacts with meiRNA 5' region in vitro and stimulates meiosis in vivo. However, the underlying mechanism still remains elusive. We first employed an in vitro crosslinking and immunoprecipitation sequencing (CLIP-seq) assay and demonstrated a preference for U-rich motifs of meiRNA by Mei2 RRM3. We then solved the crystal structures of Mei2 RRM3 in the apo form and complex with an 8mer RNA fragment, derived from meiRNA, as detected by in vitro CLIP-seq. These results provide structural insights into Mei2 RRM3-meiRNA complex and reveal that Mei2 RRM3 binds specifically to the UUC(U) sequence. Furthermore, a structure-based Mei2 mutation, Mei2F644A causes defective karyogamy, suggesting an essential role of the RNA-binding ability of Mei2 in regulating meiosis.
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Affiliation(s)
- Siyuan Shen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yanze Jian
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fudong Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Mengqi Lv
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yongrui Liu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Jihui Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Chuanhai Fu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yunyu Shi
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
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9
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Li L, Krasnykov K, Homolka D, Gos P, Mendel M, Fish RJ, Pandey RR, Pillai RS. The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m 6A recognition. Mol Cell 2022; 82:1678-1690.e12. [PMID: 35305312 DOI: 10.1016/j.molcel.2022.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
Abstract
The functional consequence of N6-methyladenosine (m6A) RNA modification is mediated by "reader" proteins of the YTH family. YTH domain-containing 2 (YTHDC2) is essential for mammalian fertility, but its molecular function is poorly understood. Here, we identify U-rich motifs as binding sites of YTHDC2 on 3' UTRs of mouse testicular RNA targets. Although its YTH domain is an m6A-binder in vitro, the YTH point mutant mice are fertile. Significantly, the loss of its 3'→5' RNA helicase activity causes mouse infertility, with the catalytic-dead mutation being dominant negative. Biochemical studies reveal that the weak helicase activity of YTHDC2 is enhanced by its interaction with the 5'→3' exoribonuclease XRN1. Single-cell transcriptomics indicate that Ythdc2 mutant mitotic germ cells transition into meiosis but accumulate a transcriptome with mixed mitotic/meiotic identity that fail to progress further into meiosis. Finally, our demonstration that ythdc2 mutant zebrafish are infertile highlights its conserved role in animal germ cell development.
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Affiliation(s)
- Lingyun Li
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Kyrylo Krasnykov
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Pascal Gos
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Mateusz Mendel
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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10
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Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m 6A binding. Genes Dev 2022; 36:180-194. [PMID: 35058317 PMCID: PMC8887132 DOI: 10.1101/gad.349190.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Mechanisms regulating meiotic progression in mammals are poorly understood. The N6-methyladenosine (m6A) reader and 3' → 5' RNA helicase YTHDC2 switches cells from mitotic to meiotic gene expression programs and is essential for meiotic entry, but how this critical cell fate change is accomplished is unknown. Here, we provide insight into its mechanism and implicate YTHDC2 in having a broad role in gene regulation during multiple meiotic stages. Unexpectedly, mutation of the m6A-binding pocket of YTHDC2 had no detectable effect on gametogenesis and mouse fertility, suggesting that YTHDC2 function is m6A-independent. Supporting this conclusion, CLIP data defined YTHDC2-binding sites on mRNA as U-rich and UG-rich motif-containing regions within 3' UTRs and coding sequences, distinct from the sites that contain m6A during spermatogenesis. Complete loss of YTHDC2 during meiotic entry did not substantially alter translation of its mRNA binding targets in whole-testis ribosome profiling assays but did modestly affect their steady-state levels. Mutation of the ATPase motif in the helicase domain of YTHDC2 did not affect meiotic entry, but it blocked meiotic prophase I progression, causing sterility. Our findings inform a model in which YTHDC2 binds transcripts independent of m6A status and regulates gene expression during multiple stages of meiosis by distinct mechanisms.
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Affiliation(s)
- Yuhki Saito
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - M Rhyan Puno
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Shreya N Sarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Christopher D Lima
- Structural Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Devanshi Jain
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey 08854, USA
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11
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Faber MW, Vo TV. Long RNA-Mediated Chromatin Regulation in Fission Yeast and Mammals. Int J Mol Sci 2022; 23:968. [PMID: 35055152 PMCID: PMC8778201 DOI: 10.3390/ijms23020968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast Schizosaccharomyces pombe (S. pombe) and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in S. pombe that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in cis and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.
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Affiliation(s)
| | - Tommy V. Vo
- Department of Biochemistry and Molecular Biology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA;
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12
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Nambu M, Kishikawa A, Yamada T, Ichikawa K, Kira Y, Itabashi Y, Honda A, Yamada K, Murakami H, Yamamoto A. Direct evaluation of cohesin-mediated sister kinetochore associations at meiosis I in fission yeast. J Cell Sci 2022; 135:jcs259102. [PMID: 34851403 DOI: 10.1242/jcs.259102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
Kinetochores drive chromosome segregation by mediating chromosome interactions with the spindle. In higher eukaryotes, sister kinetochores are separately positioned on opposite sides of sister centromeres during mitosis, but associate with each other during meiosis I. Kinetochore association facilitates the attachment of sister chromatids to the same pole, enabling the segregation of homologous chromosomes toward opposite poles. In the fission yeast, Schizosaccharomyces pombe, Rec8-containing meiotic cohesin is suggested to establish kinetochore associations by mediating cohesion of the centromere cores. However, cohesin-mediated kinetochore associations on intact chromosomes have never been demonstrated directly. In the present study, we describe a novel method for the direct evaluation of kinetochore associations on intact chromosomes in live S. pombe cells, and demonstrate that sister kinetochores and the centromere cores are positioned separately on mitotic chromosomes but associate with each other on meiosis I chromosomes. Furthermore, we demonstrate that kinetochore association depends on meiotic cohesin and the cohesin regulators Moa1 and Mrc1, and requires mating-pheromone signaling for its establishment. These results confirm cohesin-mediated kinetochore association and its regulatory mechanisms, along with the usefulness of the developed method for its analysis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Masashi Nambu
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Atsuki Kishikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Takatomi Yamada
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Kento Ichikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yunosuke Kira
- Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yuta Itabashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akira Honda
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kohei Yamada
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hiroshi Murakami
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Ayumu Yamamoto
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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13
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Birot A, Kus K, Priest E, Al Alwash A, Castello A, Mohammed S, Vasiljeva L, Kilchert C. RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response. Life Sci Alliance 2021; 5:5/2/e202101111. [PMID: 34848435 PMCID: PMC8645331 DOI: 10.26508/lsa.202101111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 11/24/2022] Open
Abstract
Comparative RNA interactome capture identifies potential regulators of RNA metabolism in fission yeast and reveals RNA exosome–dependent buffering of stress-responsive gene expression networks. The nuclear RNA exosome plays a key role in controlling the levels of multiple protein-coding and non-coding RNAs. Recruitment of the exosome to specific RNA substrates is mediated by RNA-binding co-factors. The transient interaction between co-factors and the exosome as well as the rapid decay of RNA substrates make identification of exosome co-factors challenging. Here, we use comparative poly(A)+ RNA interactome capture in fission yeast expressing three different mutants of the exosome to identify proteins that interact with poly(A)+ RNA in an exosome-dependent manner. Our analyses identify multiple RNA-binding proteins whose association with RNA is altered in exosome mutants, including the zinc-finger protein Mub1. Mub1 is required to maintain the levels of a subset of exosome RNA substrates including mRNAs encoding for stress-responsive proteins. Removal of the zinc-finger domain leads to loss of RNA suppression under non-stressed conditions, altered expression of heat shock genes in response to stress, and reduced growth at elevated temperature. These findings highlight the importance of exosome-dependent mRNA degradation in buffering gene expression networks to mediate cellular adaptation to stress.
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Affiliation(s)
- Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily Priest
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ahmad Al Alwash
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, UK.,MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
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14
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Cho SY, Jung SJ, Kim KD, Roe JH. Non-mitochondrial aconitase regulates the expression of iron-uptake genes by controlling the RNA turnover process in fission yeast. J Microbiol 2021; 59:1075-1082. [PMID: 34705258 DOI: 10.1007/s12275-021-1438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
Aconitase, a highly conserved protein across all domains of life, functions in converting citrate to isocitrate in the tricarboxylic acid cycle. Cytosolic aconitase is also known to act as an iron regulatory protein in mammals, binding to the RNA hairpin structures known as iron-responsive elements within the untranslated regions of specific RNAs. Aconitase-2 (Aco2) in fission yeast is a fusion protein consisting of an aconitase and a mitochondrial ribosomal protein, bL21, residing not only in mitochondria but also in cytosol and the nucleus. To investigate the role of Aco2 in the nucleus and cytoplasm of fission yeast, we analyzed the transcriptome of aco2ΔN mutant that is deleted of nuclear localization signal (NLS). RNA sequencing revealed that the aco2ΔN mutation caused increase in mRNAs encoding iron uptake transporters, such as Str1, Str3, and Shu1. The half-lives of mRNAs for these genes were found to be significantly longer in the aco2ΔN mutant than the wild-type strain, suggesting the role of Aco2 in mRNA turnover. The three conserved cysteines required for the catalytic activity of aconitase were not necessary for this role. The UV cross-linking RNA immunoprecipitation analysis revealed that Aco2 directly bound to the mRNAs of iron uptake transporters. Aco2-mediated degradation of iron-uptake mRNAs appears to utilize exoribonuclease pathway that involves Rrp6 as evidenced by genetic interactions. These results reveal a novel role of non-mitochondrial aconitase protein in the mRNA turnover in fission yeast to fine-tune iron homeostasis, independent of regulation by transcriptional repressor Fep1.
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Affiliation(s)
- Soo-Yeon Cho
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soo-Jin Jung
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 02841, Republic of Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Jung-Hye Roe
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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15
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Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae. Biomolecules 2021; 11:biom11081223. [PMID: 34439889 PMCID: PMC8394074 DOI: 10.3390/biom11081223] [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: 07/16/2021] [Revised: 08/05/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
Gametogenesis in diploid cells of the budding yeast Saccharomyces cerevisiae produces four haploid meiotic products called spores. Spores are dormant until nutrients trigger germination, when they bud asexually or mate to return to the diploid state. Each sporulating diploid produces a mix of spores of two haploid mating types, a and α. In asexually dividing haploids, the mating types result from distinct, mutually exclusive gene expression programs responsible for production of mating pheromones and the receptors to sense them, all of which are silent in diploids. It was assumed that spores only transcribe haploid- and mating-type-specific genes upon germination. We find that dormant spores of each mating type harbor transcripts representing all these genes, with the exception of Mata1, which we found to be enriched in a spores. Mata1 transcripts, from a rare yeast gene with two introns, were mostly unspliced. If the retained introns reflect tethering to the MATa locus, this could provide a mechanism for biased inheritance. Translation of pheromones and receptors were repressed at least until germination. We find antisense transcripts to many mating genes that may be responsible. These findings add to the growing number of examples of post-transcriptional regulation of gene expression during gametogenesis.
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16
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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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17
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Watson AT, Hassell-Hart S, Spencer J, Carr AM. Rice ( Oryza sativa) TIR1 and 5'adamantyl-IAA Significantly Improve the Auxin-Inducible Degron System in Schizosaccharomyces pombe. Genes (Basel) 2021; 12:genes12060882. [PMID: 34201031 PMCID: PMC8229956 DOI: 10.3390/genes12060882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 01/05/2023] Open
Abstract
The auxin-inducible degron (AID) system is a powerful tool to induce targeted degradation of proteins in eukaryotic model organisms. The efficiency of the existing Schizosaccharomyces pombe AID system is limited due to the fusion of the F-box protein TIR1 protein to the SCF component, Skp1 (Skp1-TIR1). Here, we report an improved AID system for S. pombe that uses the TIR1 from Oryza sativa (OsTIR1) not fused to Skp1. Furthermore, we demonstrate that degradation efficiency can be improved by pairing an OsTIR1 auxin-binding site mutant, OsTIR1F74A, with an auxin analogue, 5'adamantyl-IAA (AID2). We provide evidence for the enhanced functionality of the OsTIR1 AID and AID2 systems by application to the essential DNA replication factor Mcm4 and to a non-essential recombination protein, Rad52. Unlike AID, no detectable auxin-independent depletion of AID-tagged proteins was observed using AID2.
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Affiliation(s)
- Adam T. Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK;
| | - Storm Hassell-Hart
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK; (S.H.-H.); (J.S.)
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK; (S.H.-H.); (J.S.)
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK;
- Correspondence:
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18
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Shi R, Ying S, Li Y, Zhu L, Wang X, Jin H. Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics. Cell Death Dis 2021; 12:346. [PMID: 33795663 PMCID: PMC8016981 DOI: 10.1038/s41419-021-03625-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent and reversible modification of mRNA in mammalian cells, has recently been extensively studied in epigenetic regulation. YTH family proteins, whose YTH domain can recognize and bind m6A-containing RNA, are the main "readers" of m6A modification. YTH family proteins perform different functions to determine the metabolic fate of m6A-modified RNA. The crystal structure of the YTH domain has been completely resolved, highlighting the important roles of several conserved residues of the YTH domain in the specific recognition of m6A-modified RNAs. Upstream and downstream targets have been successively revealed in different cancer types and the role of YTH family proteins has been emphasized in m6A research. This review describes the regulation of RNAs by YTH family proteins, the structural features of the YTH domain, and the connections of YTH family proteins with human cancers.
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Affiliation(s)
- Rongkai Shi
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Shilong Ying
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Yadan Li
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Cancer Center, Zhejiang University, Hangzhou, China
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19
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Andric V, Nevers A, Hazra D, Auxilien S, Menant A, Graille M, Palancade B, Rougemaille M. A scaffold lncRNA shapes the mitosis to meiosis switch. Nat Commun 2021; 12:770. [PMID: 33536434 PMCID: PMC7859202 DOI: 10.1038/s41467-021-21032-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to the regulation of gene expression in response to intra- or extracellular signals but the underlying molecular mechanisms remain largely unexplored. Here, we identify an uncharacterized lncRNA as a central player in shaping the meiotic gene expression program in fission yeast. We report that this regulatory RNA, termed mamRNA, scaffolds the antagonistic RNA-binding proteins Mmi1 and Mei2 to ensure their reciprocal inhibition and fine tune meiotic mRNA degradation during mitotic growth. Mechanistically, mamRNA allows Mmi1 to target Mei2 for ubiquitin-mediated downregulation, and conversely enables accumulating Mei2 to impede Mmi1 activity, thereby reinforcing the mitosis to meiosis switch. These regulations also occur within a unique Mmi1-containing nuclear body, positioning mamRNA as a spatially-confined sensor of Mei2 levels. Our results thus provide a mechanistic basis for the mutual control of gametogenesis effectors and further expand our vision of the regulatory potential of lncRNAs.
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Affiliation(s)
- Vedrana Andric
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alicia Nevers
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ditipriya Hazra
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.,Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alexandra Menant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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20
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Garg A. A lncRNA-regulated gene expression system with rapid induction kinetics in the fission yeast Schizosaccharomyces pombe. RNA (NEW YORK, N.Y.) 2020; 26:1743-1752. [PMID: 32788323 PMCID: PMC7566572 DOI: 10.1261/rna.076000.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism for the study of eukaryotic cellular physiology. The organism is genetically tractable and several tools to study the functions of individual genes are available. One such tool is regulatable gene expression and overproduction of proteins. Limitations of currently available overexpression systems include delay in expression after induction, narrow dynamic range, and system-wide changes due to induction conditions. Here I describe a new long noncoding RNA (lncRNA)-regulated, thiamine-inducible expression system that integrates lncRNA-based transcriptional interference at the fission yeast tgp1 promoter with the fast repression kinetics of the thiamine-repressible nmt1 promoter. This hybrid system has rapid induction kinetics, broad dynamic range, and tunable expression via thiamine concentration. The lncRNA-regulated thiamine-inducible system will be advantageous for the study of individual genes and for potential applications in the production of heterologous proteins in fission yeast.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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21
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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22
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Kilchert C, Kecman T, Priest E, Hester S, Aydin E, Kus K, Rossbach O, Castello A, Mohammed S, Vasiljeva L. System-wide analyses of the fission yeast poly(A) + RNA interactome reveal insights into organization and function of RNA-protein complexes. Genome Res 2020; 30:1012-1026. [PMID: 32554781 PMCID: PMC7397868 DOI: 10.1101/gr.257006.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/18/2020] [Indexed: 01/12/2023]
Abstract
Large RNA-binding complexes play a central role in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA–protein crosslinking data provide information on the organization of RNA–protein complexes. To evaluate the relative enrichment of cellular RBPs on poly(A)+ RNA, we combine poly(A)+ RNA interactome capture with a whole-cell extract normalization procedure. This approach yields estimates of in vivo RNA-binding activities that identify subunits within multiprotein complexes that directly contact RNA. As validation, we trace RNA interactions of different functional modules of the 3′ end processing machinery and reveal additional contacts. Extending our analysis to different mutants of the RNA exosome complex, we explore how substrate channeling through the complex is affected by mutation. Our data highlight the central role of the RNA helicase Mtl1 in regulation of the complex and provide insights into how different components contribute to engagement of the complex with substrate RNA. In addition, we characterize RNA-binding activities of novel RBPs that have been recurrently detected in the RNA interactomes of multiple species. We find that many of these, including cyclophilins and thioredoxins, are substoichiometric RNA interactors in vivo. Because RBPomes show very good overall agreement between species, we propose that the RNA-binding characteristics we observe in fission yeast are likely to apply to related proteins in higher eukaryotes as well.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Emily Priest
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Svenja Hester
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Ebru Aydin
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Oliver Rossbach
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.,Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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23
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Thillainadesan G, Xiao H, Holla S, Dhakshnamoorthy J, Jenkins LMM, Wheeler D, Grewal SIS. Conserved protein Pir2 ARS2 mediates gene repression through cryptic introns in lncRNAs. Nat Commun 2020; 11:2412. [PMID: 32415063 PMCID: PMC7229227 DOI: 10.1038/s41467-020-16280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are components of epigenetic control mechanisms that ensure appropriate and timely gene expression. The functions of lncRNAs are often mediated through associated gene regulatory activities, but how lncRNAs are distinguished from other RNAs and recruit effector complexes is unclear. Here, we utilize the fission yeast Schizosaccharomyces pombe to investigate how lncRNAs engage silencing activities to regulate gene expression in cis. We find that invasion of lncRNA transcription into the downstream gene body incorporates a cryptic intron required for repression of that gene. Our analyses show that lncRNAs containing cryptic introns are targeted by the conserved Pir2ARS2 protein in association with splicing factors, which recruit RNA processing and chromatin-modifying activities involved in gene silencing. Pir2 and splicing machinery are broadly required for gene repression. Our finding that human ARS2 also interacts with splicing factors suggests a conserved mechanism mediates gene repression through cryptic introns within lncRNAs. In fission yeast, several lncRNAs act in cis to regulate expression of adjacent genes. Here, the authors show that the conserved Pir2ARS2 protein is targeted, along with splicing factors, to cryptic introns in lncRNAs and recruits effectors, including RNAi machinery, for gene repression.
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Affiliation(s)
- Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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24
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Krapp A, Hamelin R, Armand F, Chiappe D, Krapp L, Cano E, Moniatte M, Simanis V. Analysis of the S. pombe Meiotic Proteome Reveals a Switch from Anabolic to Catabolic Processes and Extensive Post-transcriptional Regulation. Cell Rep 2020; 26:1044-1058.e5. [PMID: 30673600 DOI: 10.1016/j.celrep.2018.12.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/09/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022] Open
Abstract
Meiotic progression in S. pombe is regulated by stage-specific gene expression and translation, changes in RNA stability, expression of anti-sense transcripts, and targeted proteolysis of regulatory proteins. We have used SILAC labeling to examine the relative levels of proteins in diploid S. pombe cells during meiosis. Among the 3,268 proteins quantified at all time points, the levels of 880 proteins changed at least 2-fold; the majority of proteins showed stepwise increases or decreases during the meiotic divisions, while some changed transiently. Overall, we observed reductions in proteins involved in anabolism and increases in proteins involved in catabolism. We also observed increases in the levels of proteins of the ESCRT-III complex and revealed a role for ESCRT-III components in chromosome segregation and spore formation. Correlation with studies of meiotic gene expression and ribosome occupancy reveals that many of the changes in steady-state protein levels are post-transcriptional.
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Affiliation(s)
- Andrea Krapp
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland
| | - Romain Hamelin
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Florence Armand
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Diego Chiappe
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Lucien Krapp
- EPFL SV IBI-SV UPDALPE, AAB 1 17, Station 19, 1015 Lausanne, Switzerland
| | - Elena Cano
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland
| | - Marc Moniatte
- EPFL Proteomics Core Facility, EPFL SV PTECH PTP, AI 0149, Station 15, 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, 1015 Lausanne, Switzerland.
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25
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Chaudhuri A, Das S, Das B. Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1591. [PMID: 32101377 DOI: 10.1002/wrna.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Intracellular trafficking and localization of mRNAs provide a mechanism of regulation of expression of genes with excellent spatial control. mRNA localization followed by localized translation appears to be a mechanism of targeted protein sorting to a specific cell-compartment, which is linked to the establishment of cell polarity, cell asymmetry, embryonic axis determination, and neuronal plasticity in metazoans. However, the complexity of the mechanism and the components of mRNA localization in higher organisms prompted the use of the unicellular organism Saccharomyces cerevisiae as a simplified model organism to study this vital process. Current knowledge indicates that a variety of mRNAs are asymmetrically and selectively localized to the tip of the bud of the daughter cells, to the vicinity of endoplasmic reticulum, mitochondria, and nucleus in this organism, which are connected to diverse cellular processes. Interestingly, specific cis-acting RNA localization elements (LEs) or RNA zip codes play a crucial role in the localization and trafficking of these localized mRNAs by providing critical binding sites for the specific RNA-binding proteins (RBPs). In this review, we present a comprehensive account of mRNA localization in S. cerevisiae, various types of localization elements influencing the mRNA localization, and the RBPs, which bind to these LEs to implement a number of vital physiological processes. Finally, we emphasize the significance of this process by highlighting their connection to several neuropathological disorders and cancers. This article is categorized under: RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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26
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Meiotic gene silencing complex MTREC/NURS recruits the nuclear exosome to YTH-RNA-binding protein Mmi1. PLoS Genet 2020; 16:e1008598. [PMID: 32012158 PMCID: PMC7018101 DOI: 10.1371/journal.pgen.1008598] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/13/2020] [Accepted: 01/03/2020] [Indexed: 11/24/2022] Open
Abstract
Accurate target recognition in transcript degradation is crucial for regulation of gene expression. In the fission yeast Schizosaccharomyces pombe, a number of meiotic transcripts are recognized by a YTH-family RNA-binding protein, Mmi1, and selectively degraded by the nuclear exosome during mitotic growth. Mmi1 forms nuclear foci in mitotically growing cells, and the nuclear exosome colocalizes to such foci. However, it remains elusive how Mmi1 and the nuclear exosome are connected. Here, we show that a complex called MTREC (Mtl1-Red1 core) or NURS (nuclear RNA silencing) that consists of a zinc-finger protein, Red1, and an RNA helicase, Mtl1, is required for the recruitment of the nuclear exosome to Mmi1 foci. Physical interaction between Mmi1 and the nuclear exosome depends on Red1. Furthermore, a chimeric protein involving Mmi1 and Rrp6, which is a nuclear-specific component of the exosome, suppresses the ectopic expression phenotype of meiotic transcripts in red1Δ cells and mtl1 mutant cells. These data indicate that the primary function of MTREC/NURS in meiotic transcript elimination is to link Mmi1 to the nuclear exosome physically. Since abnormal gene expression is detrimental to proliferation, cells possess a number of mechanisms to regulate gene expression at transcriptional and post-transcriptional levels. In particular, expression of meiotic genes is rigorously repressed in somatic cells because their aberrant expression causes severe cellular defects including genome instability and tumorigenesis. In the fission yeast Schizosaccharomyces pombe, selective degradation of meiotic transcripts is employed to prevent their deleterious expression during mitotic growth. Meiotic transcripts are recognized by a YTH-family RNA-binding protein, Mmi1. Mmi1 then induces their selective degradation by the nuclear exosome, which is a highly conserved exonuclease complex. However, little is known how Mmi1 cooperates with the nuclear exosome. Here, we demonstrate that the interaction of Mmi1 with the nuclear exosome is mediated by a complex termed MTREC/NURS that is composed of a conserved zinc-finger protein, Red1, and an RNA helicase, Mtl1. Our findings shed light on the target recognition mechanisms of post-transcriptional regulation.
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27
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Formation of S. pombe Erh1 homodimer mediates gametogenic gene silencing and meiosis progression. Sci Rep 2020; 10:1034. [PMID: 31974447 PMCID: PMC6978305 DOI: 10.1038/s41598-020-57872-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/23/2019] [Indexed: 11/17/2022] Open
Abstract
Timely and accurate expression of the genetic information relies on the integration of environmental cues and the activation of regulatory networks involving transcriptional and post-transcriptional mechanisms. In fission yeast, meiosis-specific transcripts are selectively targeted for degradation during mitosis by the EMC complex, composed of Erh1, the ortholog of human ERH, and the YTH family RNA-binding protein Mmi1. Here, we present the crystal structure of Erh1 and show that it assembles as a homodimer. Mutations of amino acid residues to disrupt Erh1 homodimer formation result in loss-of-function phenotypes, similar to erh1∆ cells: expression of meiotic genes is derepressed in mitotic cells and meiosis progression is severely compromised. Interestingly, formation of Erh1 homodimer is dispensable for interaction with Mmi1, suggesting that only fully assembled EMC complexes consisting of two Mmi1 molecules bridged by an Erh1 dimer are functionally competent. We also show that Erh1 does not contribute to Mmi1-dependent down-regulation of the meiosis regulator Mei2, supporting the notion that Mmi1 performs additional functions beyond EMC. Overall, our results provide a structural basis for the assembly of the EMC complex and highlight its biological relevance in gametogenic gene silencing and meiosis progression.
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28
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Kilchert C, Hester S, Castello A, Mohammed S, Vasiljeva L. Comparative Poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants. Methods Mol Biol 2020; 2062:255-276. [PMID: 31768981 DOI: 10.1007/978-1-4939-9822-7_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA exosome complexes degrade many different RNA substrates. Substrate selection and targeting to the exosome complex rely on cofactors, which bind to the substrate RNA, recruit the exosome complex, and help to remodel the associated ribonucleoprotein particle to facilitate RNA degradation. These cofactors are RNA-binding proteins, but their interaction with RNA may be very transient because the RNAs they are bound to are rapidly turned over by the exosome complex. Hence, the cofactors involved in the degradation of many exosome substrates are unknown. Here, we describe comparative poly(A)+ RNA interactome capture as a method to screen for novel RNA-binding proteins involved in exosome-dependent RNA decay.For this, we compare the poly(A)+ RNA interactome of wild-type cells to that of RNA surveillance mutants, where the decay of exosome substrates is compromised and occupancy of exosome cofactors on RNA is strongly increased. More specifically, protein-RNA complexes in wild-type and mutant cells are UV-cross-linked in vivo after labeling with the photoactivatable nucleoside analogue 4-thiouracil. Following cell lysis, protein-RNA complexes are selected on oligo d(T) beads, subjected to stringent washes, and eluted in a low salt buffer. After RNase digestion of cross-linked RNA, RNA-binding proteins that are enriched in the mutant samples are identified by quantitative mass spectrometry. Here, we quantitatively compare the RNA-protein interactomes of wild-type and rrp6Δ cells to selectively determine cofactors of the nuclear RNA exosome complex in fission yeast. With minor modifications, the comparative interactome approach can easily be adapted to study a range of different RNA-dependent processes in various cellular systems.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Svenja Hester
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford, UK.
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29
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Silla T, Karadoulama E, Mąkosa D, Lubas M, Jensen TH. The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts. Cell Rep 2019; 23:2199-2210. [PMID: 29768216 PMCID: PMC5972229 DOI: 10.1016/j.celrep.2018.04.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/15/2018] [Indexed: 12/31/2022] Open
Abstract
Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA+) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA+ RNA foci with “pA-tail exosome targeting (PAXT) connection” components MTR4, ZFC3H1, and PABPN1 but no overlap with known nuclear structures such as Cajal bodies, speckles, paraspeckles, or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence, selected pA+ RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear pA+ RNA retention factor, counteracting nuclear export activity. Abolished RNA exosome function leads to pA+ RNA accumulation in nuclear foci pA+ RNA foci are enriched with various transcripts and exosome adaptor proteins The exosome adaptor protein ZFC3H1 is required for pA+ RNA foci formation ZFC3H1 functionally counteracts the mRNA export factor AlyREF
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Affiliation(s)
- Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark; The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloesvej 5, 2200 Copenhagen, Denmark
| | - Dawid Mąkosa
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Michal Lubas
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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30
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Sorida M, Murakami Y. Unprogrammed epigenetic variation mediated by stochastic formation of ectopic heterochromatin. Curr Genet 2019; 66:319-325. [PMID: 31598751 DOI: 10.1007/s00294-019-01031-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023]
Abstract
Changes in gene expression via chromatin-mediated mechanisms are important for reprogramming and differentiation, but uncontrolled changes can potentially lead to harmful or adaptive phenotypic alteration. Thus, diversification of the genome-wide chromatin state must be strictly limited, but the underlying mechanism of this regulation is largely unknown. In this review, we focused on distribution of heterochromatin, a tight chromatin structure that negatively regulates gene expression. Heterochromatin is characterized by methylation of histone H3 at lysine 9, and its formation and spreading are controlled by H3K9-specific methyltransferases and reversal factors such as histone demethylases. We summarize recent findings and discuss how variability in the heterochromatin distribution is controlled in the unicellular eukaryote fission yeast. In this context, we recently found that the anti-silencing factor Epe1 plays a key role in the formation of the individual-specific heterochromatin distribution. In conclusion, recent studies revealed that there are many potential heterochromatin formation sites in the fission yeast genome, and several proteins contribute to suppression of spreading and genome-wide dispersal of heterochromatin; knowledge from fission yeast studies may provide insights into the mechanisms regulating epigenetic diversification in multicellular eukaryotes.
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Affiliation(s)
- Masato Sorida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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31
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meiRNA, A Polyvalent Player in Fission Yeast Meiosis. Noncoding RNA 2019; 5:ncrna5030045. [PMID: 31533287 PMCID: PMC6789587 DOI: 10.3390/ncrna5030045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 11/17/2022] Open
Abstract
A growing number of recent studies have revealed that non-coding RNAs play a wide variety of roles beyond expectation. A lot of non-coding RNAs have been shown to function by forming intracellular structures either in the nucleus or the cytoplasm. In the fission yeast Schizosaccharomyces pombe, a non-coding RNA termed meiRNA has been shown to play multiple vital roles in the course of meiosis. meiRNA is tethered to its genetic locus after transcription and forms a peculiar intranuclear dot structure. It ensures stable expression of meiotic genes in cooperation with an RNA-binding protein Mei2. Chromosome-associated meiRNA also facilitates recognition of homologous chromosome loci and induces robust pairing. In this review, the quarter-century history of meiRNA, from its identification to functional characterization, will be outlined.
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32
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Das S, Biswas S, Chaudhuri S, Bhattacharyya A, Das B. A Nuclear Zip Code in SKS1 mRNA Promotes Its Slow Export, Nuclear Retention, and Degradation by the Nuclear Exosome/DRN in Saccharomyces cerevisiae. J Mol Biol 2019; 431:3626-3646. [DOI: 10.1016/j.jmb.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 01/12/2023]
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33
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Lange H, Ndecky SYA, Gomez-Diaz C, Pflieger D, Butel N, Zumsteg J, Kuhn L, Piermaria C, Chicher J, Christie M, Karaaslan ES, Lang PLM, Weigel D, Vaucheret H, Hammann P, Gagliardi D. RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nat Commun 2019; 10:3871. [PMID: 31455787 PMCID: PMC6711988 DOI: 10.1038/s41467-019-11807-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/05/2019] [Indexed: 02/01/2023] Open
Abstract
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans. Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.
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Affiliation(s)
- Heike Lange
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Simon Y A Ndecky
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Carlos Gomez-Diaz
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Nicolas Butel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Julie Zumsteg
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Michael Christie
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ezgi S Karaaslan
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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34
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Xie G, Vo TV, Thillainadesan G, Holla S, Zhang B, Jiang Y, Lv M, Xu Z, Wang C, Balachandran V, Shi Y, Li F, Grewal SIS. A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing. Nat Commun 2019; 10:251. [PMID: 30651569 PMCID: PMC6335422 DOI: 10.1038/s41467-018-08273-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022] Open
Abstract
Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1∆ due to termination defects are revealed in mmi1W112A. Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.
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Affiliation(s)
- Guodong Xie
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beibei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Mengqi Lv
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Zheng Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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35
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Schmid M, Jensen TH. The Nuclear RNA Exosome and Its Cofactors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:113-132. [PMID: 31811632 DOI: 10.1007/978-3-030-31434-7_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The RNA exosome is a highly conserved ribonuclease endowed with 3'-5' exonuclease and endonuclease activities. The multisubunit complex resides in both the nucleus and the cytoplasm, with varying compositions and activities between the two compartments. While the cytoplasmic exosome functions mostly in mRNA quality control pathways, the nuclear RNA exosome partakes in the 3'-end processing and complete decay of a wide variety of substrates, including virtually all types of noncoding (nc) RNAs. To handle these diverse tasks, the nuclear exosome engages with dedicated cofactors, some of which serve as activators by stimulating decay through oligoA addition and/or RNA helicase activities or, as adaptors, by recruiting RNA substrates through their RNA-binding capacities. Most nuclear exosome cofactors contain the essential RNA helicase Mtr4 (MTR4 in humans). However, apart from Mtr4, nuclear exosome cofactors have undergone significant evolutionary divergence. Here, we summarize biochemical and functional knowledge about the nuclear exosome and exemplify its cofactor variety by discussing the best understood model organisms-the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and human cells.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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36
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Mukherjee K, Futcher B, Leatherwood J. mmi1 and rep2 mRNAs are novel RNA targets of the Mei2 RNA-binding protein during early meiosis in Schizosaccharomyces pombe. Open Biol 2018; 8:rsob.180110. [PMID: 30257894 PMCID: PMC6170507 DOI: 10.1098/rsob.180110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/28/2018] [Indexed: 11/12/2022] Open
Abstract
The RNA-binding protein Mei2 is crucial for meiosis in Schizosaccharomyces pombe. In mei2 mutants, pre-meiotic S-phase is blocked, along with meiosis. Mei2 binds a long non-coding RNA (lncRNA) called meiRNA, which is a 'sponge RNA' for the meiotic inhibitor protein Mmi1. The interaction between Mei2, meiRNA and Mmi1 protein is essential for meiosis. But mei2 mutants have stronger and different phenotypes than meiRNA mutants, since mei2Δ arrests before pre-meiotic S, while the meiRNA mutant arrests after pre-meiotic S but before meiosis. This suggests Mei2 may bind additional RNAs. To identify novel RNA targets of Mei2, which might explain how Mei2 regulates pre-meiotic S, we used RNA immunoprecipitation and cross-linking immunoprecipitation. In addition to meiRNA, we found the mRNAs for mmi1 (which encodes Mmi1) and for the S-phase transcription factor rep2 There were also three other RNAs of uncertain relevance. We suggest that at meiotic initiation, Mei2 may sequester rep2 mRNA to help allow pre-meiotic S, and then may bind both meiRNA and mmi1 mRNA to inactivate Mmi1 at two levels, the protein level (as previously known), and also the mRNA level, allowing meiosis. We call Mei2-meiRNA a 'double sponge' (i.e. binding both an mRNA and its encoded protein).
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Affiliation(s)
- Kaustav Mukherjee
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
| | - Janet Leatherwood
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
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37
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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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38
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A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol 2018; 102:7319-7331. [PMID: 29974182 PMCID: PMC6097775 DOI: 10.1007/s00253-018-9187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.
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39
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Stowell JAW, Wagstaff JL, Hill CH, Yu M, McLaughlin SH, Freund SMV, Passmore LA. A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding. J Biol Chem 2018; 293:9210-9222. [PMID: 29695507 PMCID: PMC6005420 DOI: 10.1074/jbc.ra118.002291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/19/2018] [Indexed: 01/12/2023] Open
Abstract
Mmi1 is an essential RNA-binding protein in the fission yeast Schizosaccharomyces pombe that eliminates meiotic transcripts during normal vegetative growth. Mmi1 contains a YTH domain that binds specific RNA sequences, targeting mRNAs for degradation. The YTH domain of Mmi1 uses a noncanonical RNA-binding surface that includes contacts outside the conserved fold. Here, we report that an N-terminal extension that is proximal to the YTH domain enhances RNA binding. Using X-ray crystallography, NMR, and biophysical methods, we show that this low-complexity region becomes more ordered upon RNA binding. This enhances the affinity of the interaction of the Mmi1 YTH domain with specific RNAs by reducing the dissociation rate of the Mmi1-RNA complex. We propose that the low-complexity region influences RNA binding indirectly by reducing dynamic motions of the RNA-binding groove and stabilizing a conformation of the YTH domain that binds to RNA with high affinity. Taken together, our work reveals how a low-complexity region proximal to a conserved folded domain can adopt an ordered structure to aid nucleic acid binding.
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Affiliation(s)
- James A W Stowell
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Jane L Wagstaff
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Chris H Hill
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Minmin Yu
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | | | - Stefan M V Freund
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Lori A Passmore
- From the MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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40
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Abstract
The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation and cell differentiation. In this review, we summarize the current knowledge of the mechanisms of nuclear exosome-mediated RNA metabolism and discuss their physiological significance.
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41
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Shichino Y, Otsubo Y, Kimori Y, Yamamoto M, Yamashita A. YTH-RNA-binding protein prevents deleterious expression of meiotic proteins by tethering their mRNAs to nuclear foci. eLife 2018; 7:32155. [PMID: 29424342 PMCID: PMC5807050 DOI: 10.7554/elife.32155] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/31/2018] [Indexed: 12/24/2022] Open
Abstract
Accurate and extensive regulation of meiotic gene expression is crucial to distinguish germ cells from somatic cells. In the fission yeast Schizosaccharomyces pombe, a YTH family RNA-binding protein, Mmi1, directs the nuclear exosome-mediated elimination of meiotic transcripts during vegetative proliferation. Mmi1 also induces the formation of facultative heterochromatin at a subset of its target genes. Here, we show that Mmi1 prevents the mistimed expression of meiotic proteins by tethering their mRNAs to the nuclear foci. Mmi1 interacts with itself with the assistance of a homolog of Enhancer of Rudimentary, Erh1. Mmi1 self-interaction is required for foci formation, target transcript elimination, their nuclear retention, and protein expression inhibition. We propose that nuclear foci formed by Mmi1 are not only the site of RNA degradation, but also of sequestration of meiotic transcripts from the translation machinery.
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Affiliation(s)
- Yuichi Shichino
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan
| | - Yoko Otsubo
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan.,Laboratory of Biological Diversity, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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42
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Sanchez AM, Shuman S, Schwer B. Poly(A) site choice and Pol2 CTD Serine-5 status govern lncRNA control of phosphate-responsive tgp1 gene expression in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:237-250. [PMID: 29122971 PMCID: PMC5769750 DOI: 10.1261/rna.063966.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/09/2017] [Indexed: 05/24/2023]
Abstract
Expression of fission yeast glycerophosphate transporter Tgp1 is repressed in phosphate-rich medium and induced during phosphate starvation. Repression is enforced by transcription of the nc-tgp1 locus upstream of tgp1 to produce a long noncoding (lnc) RNA. Here we identify two essential elements of the nc-tgp1 promoter: a TATA box -30TATATATA-23 and a HomolD box -64CAGTCACA-57, mutations of which inactivate the nc-tgp1 promoter and de-repress the downstream tgp1 promoter under phosphate-replete conditions. The nc-tgp1 lncRNA poly(A) site maps to nucleotide +1636 of the transcription unit, which coincides with the binding site for Pho7 (1632TCGGACATTCAA1643), the transcription factor that drives tgp1 expression. Overlap between the lncRNA template and the tgp1 promoter points to transcriptional interference as the simplest basis for lncRNA repression. We identify a shorter RNA derived from the nc-tgp1 locus, polyadenylated at position +508, well upstream of the tgp1 promoter. Mutating the nc-tgp1-short RNA polyadenylation signal abolishes de-repression of the downstream tgp1 promoter elicited by Pol2 CTD Ser5Ala phospho-site mutation. Ser5 mutation favors utilization of the short RNA poly(A) site, thereby diminishing transcription of the lncRNA that interferes with the tgp1 promoter. Mutating the nc-tgp1-short RNA polyadenylation signal attenuates induction of the tgp1 promoter during phosphate starvation. Polyadenylation site choice governed by CTD Ser5 status adds a new level of lncRNA control of gene expression and reveals a new feature of the fission yeast CTD code.
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Affiliation(s)
- Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
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43
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Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S. ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. eLife 2018; 7:30919. [PMID: 29360036 PMCID: PMC5832417 DOI: 10.7554/elife.30919] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, ‘ketu’, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
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Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - M Rhyan Puno
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States.,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
| | - Christopher D Lima
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kathryn V Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
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44
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Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1. Cell Rep 2017; 17:1978-1989. [PMID: 27851962 PMCID: PMC5120349 DOI: 10.1016/j.celrep.2016.10.066] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/10/2016] [Accepted: 10/19/2016] [Indexed: 12/22/2022] Open
Abstract
Ccr4-Not is a conserved protein complex that shortens the 3' poly(A) tails of eukaryotic mRNAs to regulate transcript stability and translation into proteins. RNA-binding proteins are thought to facilitate recruitment of Ccr4-Not to certain mRNAs, but lack of an in-vitro-reconstituted system has slowed progress in understanding the mechanistic details of this specificity. Here, we generate a fully recombinant Ccr4-Not complex that removes poly(A) tails from RNA substrates. The intact complex is more active than the exonucleases alone and has an intrinsic preference for certain RNAs. The RNA-binding protein Mmi1 is highly abundant in preparations of native Ccr4-Not. We demonstrate a high-affinity interaction between recombinant Ccr4-Not and Mmi1. Using in vitro assays, we show that Mmi1 accelerates deadenylation of target RNAs. Together, our results support a model whereby both RNA-binding proteins and the sequence context of mRNAs influence deadenylation rate to regulate gene expression.
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45
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Wu B, Xu J, Su S, Liu H, Gan J, Ma J. Structural insights into the specific recognition of DSR by the YTH domain containing protein Mmi1. Biochem Biophys Res Commun 2017; 491:310-316. [DOI: 10.1016/j.bbrc.2017.07.104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 01/01/2023]
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46
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Yamashita A, Sakuno T, Watanabe Y, Yamamoto M. Analysis of Schizosaccharomyces pombe Meiosis. Cold Spring Harb Protoc 2017; 2017:pdb.top079855. [PMID: 28733417 DOI: 10.1101/pdb.top079855] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Meiosis is a specialized cell cycle that generates haploid gametes from diploid cells. The fission yeast Schizosaccharomyces pombe is one of the best model organisms for studying the regulatory mechanisms of meiosis. S. pombe cells, which normally grow in the haploid state, diploidize by conjugation and initiate meiosis when starved for nutrients, especially nitrogen. Following two rounds of chromosome segregation, spore formation takes place. The switch from mitosis to meiosis is controlled by a kinase, Pat1, and an RNA-binding protein, Mei2. Mei2 is also a key factor for meiosis-specific gene expression. Studies on S. pombe have offered insights into cell cycle regulation and chromosome segregation during meiosis. Here we outline the current understanding of the molecular mechanisms regulating the initiation and progression of meiosis, and introduce methods for the study of meiosis in fission yeast.
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Affiliation(s)
- Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan;
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Sakuno
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Yoshinori Watanabe
- Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Tokyo 113-0032, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan;
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi 444-8585, Japan
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47
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Simonetti F, Candelli T, Leon S, Libri D, Rougemaille M. Ubiquitination-dependent control of sexual differentiation in fission yeast. eLife 2017; 6:28046. [PMID: 28841135 PMCID: PMC5614563 DOI: 10.7554/elife.28046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/21/2017] [Indexed: 01/03/2023] Open
Abstract
In fission yeast, meiosis-specific transcripts are selectively eliminated during vegetative growth by the combined action of the YTH-family RNA-binding protein Mmi1 and the nuclear exosome. Upon nutritional starvation, the master regulator of meiosis Mei2 inactivates Mmi1, thereby allowing expression of the meiotic program. Here, we show that the E3 ubiquitin ligase subunit Not4/Mot2 of the evolutionarily conserved Ccr4-Not complex, which associates with Mmi1, promotes suppression of meiotic transcripts expression in mitotic cells. Our analyses suggest that Mot2 directs ubiquitination of Mei2 to preserve the activity of Mmi1 during vegetative growth. Importantly, Mot2 is not involved in the constitutive pathway of Mei2 turnover, but rather plays a regulatory role to limit its accumulation or inhibit its function. We propose that Mmi1 recruits the Ccr4-Not complex to counteract its own inhibitor Mei2, thereby locking the system in a stable state that ensures the repression of the meiotic program by Mmi1.
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Affiliation(s)
- Fabrizio Simonetti
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tito Candelli
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sebastien Leon
- Institut Jacques Monod, Team "Membrane Trafficking, Ubiquitin and Signaling", CNRS, UMR9198, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Mathieu Rougemaille
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
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48
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Abstract
This article provides an overview of sexual reproduction in the ascomycetes, a phylum of fungi that is named after the specialized sacs or "asci" that hold the sexual spores. They have therefore also been referred to as the Sac Fungi due to these characteristic structures that typically contain four to eight ascospores. Ascomycetes are morphologically diverse and include single-celled yeasts, filamentous fungi, and more complex cup fungi. The sexual cycles of many species, including those of the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe and the filamentous saprobes Neurospora crassa, Aspergillus nidulans, and Podospora anserina, have been examined in depth. In addition, sexual or parasexual cycles have been uncovered in important human pathogens such as Candida albicans and Aspergillus fumigatus, as well as in plant pathogens such as Fusarium graminearum and Cochliobolus heterostrophus. We summarize what is known about sexual fecundity in ascomycetes, examine how structural changes at the mating-type locus dictate sexual behavior, and discuss recent studies that reveal that pheromone signaling pathways can be repurposed to serve cellular roles unrelated to sex.
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49
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Touat-Todeschini L, Shichino Y, Dangin M, Thierry-Mieg N, Gilquin B, Hiriart E, Sachidanandam R, Lambert E, Brettschneider J, Reuter M, Kadlec J, Pillai R, Yamashita A, Yamamoto M, Verdel A. Selective termination of lncRNA transcription promotes heterochromatin silencing and cell differentiation. EMBO J 2017; 36:2626-2641. [PMID: 28765164 DOI: 10.15252/embj.201796571] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/14/2017] [Accepted: 06/19/2017] [Indexed: 01/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) regulating gene expression at the chromatin level are widespread among eukaryotes. However, their functions and the mechanisms by which they act are not fully understood. Here, we identify new fission yeast regulatory lncRNAs that are targeted, at their site of transcription, by the YTH domain of the RNA-binding protein Mmi1 and degraded by the nuclear exosome. We uncover that one of them, nam1, regulates entry into sexual differentiation. Importantly, we demonstrate that Mmi1 binding to this lncRNA not only triggers its degradation but also mediates its transcription termination, thus preventing lncRNA transcription from invading and repressing the downstream gene encoding a mitogen-activated protein kinase kinase kinase (MAPKKK) essential to sexual differentiation. In addition, we show that Mmi1-mediated termination of lncRNA transcription also takes place at pericentromeric regions where it contributes to heterochromatin gene silencing together with RNA interference (RNAi). These findings reveal an important role for selective termination of lncRNA transcription in both euchromatic and heterochromatic lncRNA-based gene silencing processes.
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Affiliation(s)
- Leila Touat-Todeschini
- Institut for Advanced Biosciences, UMR InsermU1209/CNRS5309/UGA, University of Grenoble Alpes, Grenoble, France
| | - Yuichi Shichino
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Mathieu Dangin
- Institut for Advanced Biosciences, UMR InsermU1209/CNRS5309/UGA, University of Grenoble Alpes, Grenoble, France
| | - Nicolas Thierry-Mieg
- TIMC-IMAG, University of Grenoble Alpes, Grenoble, France.,CNRS, TIMC-IMAG, UMR CNRS 5525, Grenoble, France
| | - Benoit Gilquin
- CEA, LETI, CLINATEC, MINATEC Campus, University of Grenoble Alpes, Grenoble, France
| | - Edwige Hiriart
- Institut for Advanced Biosciences, UMR InsermU1209/CNRS5309/UGA, University of Grenoble Alpes, Grenoble, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, New York, NY, USA
| | - Emeline Lambert
- Institut for Advanced Biosciences, UMR InsermU1209/CNRS5309/UGA, University of Grenoble Alpes, Grenoble, France
| | - Janine Brettschneider
- European Molecular Biology Laboratory, Grenoble Outstation, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France.,Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Michael Reuter
- European Molecular Biology Laboratory, Grenoble Outstation, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France.,Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Jan Kadlec
- European Molecular Biology Laboratory, Grenoble Outstation, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France.,Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, Grenoble, France.,Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Ramesh Pillai
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes, Grenoble, France.,Department of Molecular Biology, University of Geneva, Geneva 4, Switzerland
| | - Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - André Verdel
- Institut for Advanced Biosciences, UMR InsermU1209/CNRS5309/UGA, University of Grenoble Alpes, Grenoble, France
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50
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Marayati BF, Hoskins V, Boger RW, Tucker JF, Fishman ES, Bray AS, Zhang K. The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis. RNA (NEW YORK, N.Y.) 2016; 22:1349-59. [PMID: 27365210 PMCID: PMC4986891 DOI: 10.1261/rna.055608.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/21/2016] [Indexed: 06/06/2023]
Abstract
Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3'-5' exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes.
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Affiliation(s)
- Bahjat Fadi Marayati
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Victoria Hoskins
- Program of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Robert W Boger
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - James F Tucker
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Emily S Fishman
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Andrew S Bray
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Ke Zhang
- Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106, USA
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