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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Deng X, Yao Q, Horvath A, Jiang Z, Zhao J, Fischer T, Sugiyama T. The fission yeast ortholog of Coilin, Mug174, forms Cajal body-like nuclear condensates and is essential for cellular quiescence. Nucleic Acids Res 2024:gkae463. [PMID: 38828770 DOI: 10.1093/nar/gkae463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
The Cajal body, a nuclear condensate, is crucial for ribonucleoprotein assembly, including small nuclear RNPs (snRNPs). While Coilin has been identified as an integral component of Cajal bodies, its exact function remains unclear. Moreover, no Coilin ortholog has been found in unicellular organisms to date. This study unveils Mug174 (Meiosis-upregulated gene 174) as the Coilin ortholog in the fission yeast Schizosaccharomyces pombe. Mug174 forms phase-separated condensates in vitro and is often associated with the nucleolus and the cleavage body in vivo. The generation of Mug174 foci relies on the trimethylguanosine (TMG) synthase Tgs1. Moreover, Mug174 interacts with Tgs1 and U snRNAs. Deletion of the mug174+ gene in S. pombe causes diverse pleiotropic phenotypes, encompassing defects in vegetative growth, meiosis, pre-mRNA splicing, TMG capping of U snRNAs, and chromosome segregation. In addition, we identified weak homology between Mug174 and human Coilin. Notably, human Coilin expressed in fission yeast colocalizes with Mug174. Critically, Mug174 is indispensable for the maintenance of and transition from cellular quiescence. These findings highlight the Coilin ortholog in fission yeast and suggest that the Cajal body is implicated in cellular quiescence, thereby preventing human diseases.
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Affiliation(s)
- Xiaoling Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinglian Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Ziling Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Junjie Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australia
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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3
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Kumar M, Michael S, Alvarado-Valverde J, Zeke A, Lazar T, Glavina J, Nagy-Kanta E, Donagh J, Kalman Z, Pascarelli S, Palopoli N, Dobson L, Suarez C, Van Roey K, Krystkowiak I, Griffin J, Nagpal A, Bhardwaj R, Diella F, Mészáros B, Dean K, Davey N, Pancsa R, Chemes L, Gibson T. ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Res 2024; 52:D442-D455. [PMID: 37962385 PMCID: PMC10767929 DOI: 10.1093/nar/gkad1058] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant, especially when considering post-translational modifications. As well as being found throughout the cell as part of regulatory processes, SLiMs are extensively mimicked by intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource is a representative (not comprehensive) database. The ELM entries are created by a growing community of skilled annotators and provide an introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances in areas ranging from innate immunity to both protein and RNA degradation systems. In total, 39 classes of newly annotated motifs have been added, and another 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publications and including >700 links to experimentally determined 3D structures. In a recent development, the InterPro protein module resource now also includes ELM data. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Germany
| | - András Zeke
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Eszter Nagy-Kanta
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Juan Mac Donagh
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Zsofia E Kalman
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Stefano Pascarelli
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - László Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7, Budapest 1094, Hungary
| | - Carmen Florencia Suarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Kim Van Roey
- Health Services Research, Sciensano, Brussels, Belgium
| | - Izabella Krystkowiak
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Juan Esteban Griffin
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Anurag Nagpal
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa 403726, India
| | - Rajesh Bhardwaj
- Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kellie Dean
- School of Biochemistry and Cell Biology, 3.91 Western Gateway Building, University College Cork, Cork, Ireland
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Rita Pancsa
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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4
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [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] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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5
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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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6
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Kozlowski P. Thirty Years with ERH: An mRNA Splicing and Mitosis Factor Only or Rather a Novel Genome Integrity Protector? Cells 2023; 12:2449. [PMID: 37887293 PMCID: PMC10605862 DOI: 10.3390/cells12202449] [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: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
ERH is a 100 to about 110 aa nuclear protein with unique primary and three-dimensional structures that are very conserved from simple eukaryotes to humans, albeit some species have lost its gene, with most higher fungi being a noteworthy example. Initially, studies on Drosophila melanogaster implied its function in pyrimidine metabolism. Subsequently, research on Xenopus laevis suggested that it acts as a transcriptional repressor. Finally, studies in humans pointed to a role in pre-mRNA splicing and in mitosis but further research, also in Caenorhabditis elegans and Schizosaccharomyces pombe, demonstrated its much broader activity, namely involvement in the biogenesis of mRNA, and miRNA, piRNA and some other ncRNAs, and in repressive heterochromatin formation. ERH interacts with numerous, mostly taxon-specific proteins, like Mmi1 and Mei2 in S. pombe, PID-3/PICS-1, TOST-1 and PID-1 in C. elegans, and DGCR8, CIZ1, PDIP46/SKAR and SAFB1/2 in humans. There are, however, some common themes in this wide range of processes and partners, such as: (a) ERH homodimerizes to form a scaffold for several complexes involved in the metabolism of nucleic acids, (b) all these RNAs are RNA polymerase II transcripts, (c) pre-mRNAs, whose splicing depends on ERH, are enriched in transcripts of DNA damage response and DNA metabolism genes, and (d) heterochromatin is formed to silence unwanted transcription, e.g., from repetitive elements. Thus, it seems that ERH has been adopted for various pathways that serve to maintain genome integrity.
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Affiliation(s)
- Piotr Kozlowski
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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7
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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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8
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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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9
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Nuckolls NL, Nidamangala Srinivasa A, Mok AC, Helston RM, Bravo Núñez MA, Lange JJ, Gallagher TJ, Seidel CW, Zanders SE. S. pombe wtf drivers use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive. PLoS Genet 2022; 18:e1009847. [PMID: 36477651 PMCID: PMC9762604 DOI: 10.1371/journal.pgen.1009847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/19/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Meiotic drivers bias gametogenesis to ensure their transmission into more than half the offspring of a heterozygote. In Schizosaccharomyces pombe, wtf meiotic drivers destroy the meiotic products (spores) that do not inherit the driver from a heterozygote, thereby reducing fertility. wtf drivers encode both a Wtfpoison protein and a Wtfantidote protein using alternative transcriptional start sites. Here, we analyze how the expression and localization of the Wtf proteins are regulated to achieve drive. We show that transcriptional timing and selective protein exclusion from developing spores ensure that all spores are exposed to Wtf4poison, but only the spores that inherit wtf4 receive a dose of Wtf4antidote sufficient for survival. In addition, we show that the Mei4 transcription factor, a master regulator of meiosis, controls the expression of the wtf4poison transcript. This transcriptional regulation, which includes the use of a critical meiotic transcription factor, likely complicates the universal suppression of wtf genes without concomitantly disrupting spore viability. We propose that these features contribute to the evolutionary success of the wtf drivers.
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Affiliation(s)
- Nicole L. Nuckolls
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Ananya Nidamangala Srinivasa
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Anthony C. Mok
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- University of Missouri—Kansas City, Kansas City, Missouri, United States of America
| | - Rachel M. Helston
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | | | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Todd J. Gallagher
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Chris W. Seidel
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sarah E. Zanders
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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10
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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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11
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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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12
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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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13
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Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA (NEW YORK, N.Y.) 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
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Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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14
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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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15
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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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16
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Wang Y, Fan J, Wang J, Zhu Y, Xu L, Tong D, Cheng H. ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic Acids Res 2021; 49:10630-10643. [PMID: 34530450 PMCID: PMC8501945 DOI: 10.1093/nar/gkab774] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 01/23/2023] Open
Abstract
Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.
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Affiliation(s)
- Yimin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Fan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianshu Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Zhu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Deng Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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17
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Song X, Xu R, Sugiyama T. Two plasmid modules for introducing the auxin-inducible degron into the fission yeast Schizosaccharomyces pombe by PCR-based gene targeting. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000442. [PMID: 34423281 PMCID: PMC8374545 DOI: 10.17912/micropub.biology.000442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/12/2022]
Abstract
Targeted protein degradation is a powerful approach to study and inhibit protein function in vivo. Introduction of the auxin-inducible degron (AID) system to the fission yeast Schizosaccharomyces pombe was previously reported, but, to the best of our knowledge, no plasmid for constructing AID-tagged fission yeast strains has been described so far. Here, we describe two plasmids that facilitate the introduction of the mini auxin-inducible degron (mAID) tag with a FLAG epitope or GFP by the conventional PCR-based gene targeting method. Our experimental verification indicated that PCR-based mAID tagging is straightforward and that the auxin-degron system is useful for studying essential proteins in S. pombe.
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Affiliation(s)
- Xiuyi Song
- School of Life Science and Technology, ShanghaiTech University
| | - Ruoming Xu
- School of Life Science and Technology, ShanghaiTech University
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18
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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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19
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The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain. Nat Commun 2021; 12:3456. [PMID: 34103492 PMCID: PMC8187409 DOI: 10.1038/s41467-021-23565-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/05/2021] [Indexed: 12/02/2022] Open
Abstract
Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr4 and specific adaptor complexes for RNA substrate recognition. The PAXT and MTREC complexes have recently been identified as homologous exosome adaptors in human and fission yeast, respectively. The eleven-subunit MTREC comprises the zinc-finger protein Red1 and the Mtr4 homologue Mtl1. Here, we use yeast two-hybrid and pull-down assays to derive a detailed interaction map. We show that Red1 bridges MTREC submodules and serves as the central scaffold. In the crystal structure of a minimal Mtl1/Red1 complex an unstructured region adjacent to the Red1 zinc-finger domain binds to both the Mtl1 KOW domain and stalk helices. This interaction extends the canonical interface seen in Mtr4-adaptor complexes. In vivo mutational analysis shows that this interface is essential for cell survival. Our results add to Mtr4 versatility and provide mechanistic insights into the MTREC complex. The human PAXT complex and the MTREC complex in fission yeast are important exosome cofactors, serving in the degradation of specific noncoding RNAs. Here, the authors combine structural, biochemical and in vivo methods to show how Red1 recruits the Mtl1 helicase by an interface not seen before in helicase-adaptor complexes.
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20
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Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H, Levin HL. Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Rep 2021; 30:2686-2698.e8. [PMID: 32101745 PMCID: PMC9497450 DOI: 10.1016/j.celrep.2020.01.094] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/18/2019] [Accepted: 01/27/2020] [Indexed: 11/24/2022] Open
Abstract
Heterochromatin functions as a scaffold for factors responsible for gene
silencing and chromosome segregation. Heterochromatin can be assembled by
multiple pathways, including RNAi and RNA surveillance. We identified factors
that form heterochromatin using dense profiles of transposable element
integration in Schizosaccharomyces pombe. The candidates
include a large number of essential proteins such as four canonical mRNA
cleavage and polyadenylation factors. We find that Iss1, a subunit of the
poly(A) polymerase module, plays a role in forming heterochromatin in centromere
repeats that is independent of RNAi. Genome-wide maps reveal that Iss1
accumulates at genes regulated by RNA surveillance. Iss1 interacts with RNA
surveillance factors Mmi1 and Rrp6, and importantly, Iss1 contributes to RNA
elimination that forms heterochromatin at meiosis genes. Our profile of
transposable element integration supports the model that a network of mRNA
cleavage and polyadenylation factors coordinates RNA surveillance, including the
mechanism that forms heterochromatin at meiotic genes. Lee et al. use dense profiles of transposon integration to identify genes
important for the formation of heterochromatin. Among many candidates, Iss1 is a
canonical mRNA cleavage and polyadenylation factor found to be important for
heterochromatin at meiotic genes by recruiting the nuclear exosome.
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Affiliation(s)
- Si Young Lee
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stevephen Hung
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rakesh Pathak
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oluwadamilola Bankole
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Akira Yamashita
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry L Levin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Hou H, Kyriacou E, Thadani R, Klutstein M, Chapman JH, Cooper JP. Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8. Nature 2021; 591:671-676. [PMID: 33658710 PMCID: PMC8843027 DOI: 10.1038/s41586-021-03279-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
Meiotic processes are potentially dangerous to genome stability and could be disastrous if activated in proliferative cells. Here we show that two key meiosis-defining proteins, the topoisomerase Spo11 (which forms double-strand breaks) and the meiotic cohesin Rec8, can dismantle centromeres. This dismantlement is normally observable only in mutant cells that lack the telomere bouquet, which provides a nuclear microdomain conducive to centromere reassembly1; however, overexpression of Spo11 or Rec8 leads to levels of centromere dismantlement that cannot be countered by the bouquet. Specific nucleosome remodelling factors mediate centromere dismantlement by Spo11 and Rec8. Ectopic expression of either protein in proliferating cells leads to the loss of mitotic kinetochores in both fission yeast and human cells. Hence, while centromeric chromatin has been characterized as extraordinarily stable, Spo11 and Rec8 challenge this stability and may jeopardize kinetochores in cancers that express meiotic proteins.
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Affiliation(s)
- Haitong Hou
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, Phone 303-724-3203,Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892,Co-corresponding authors: ;
| | - Eftychia Kyriacou
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892,Current address: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Rahul Thadani
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, Phone 303-724-3203,Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892
| | - Michael Klutstein
- Chromatin and Aging Research Laboratory, Institute of Dental Science, Hebrew University of Jerusalem PO 12272, Israel 91120
| | - Joseph H. Chapman
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892,Current address: Single Molecular Biophysics Laboratory, NHLBI, NIH
| | - Julia Promisel Cooper
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, Phone 303-724-3203,Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892,Co-corresponding authors: ;
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22
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TOR targets an RNA processing network to regulate facultative heterochromatin, developmental gene expression and cell proliferation. Nat Cell Biol 2021; 23:243-256. [PMID: 33574613 PMCID: PMC9260697 DOI: 10.1038/s41556-021-00631-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023]
Abstract
Cell proliferation and differentiation require signalling pathways that enforce appropriate and timely gene expression. We find that Tor2, the catalytic subunit of the TORC1 complex in fission yeast, targets a conserved nuclear RNA elimination network, particularly the serine and proline-rich protein Pir1, to control gene expression through RNA decay and facultative heterochromatin assembly. Phosphorylation by Tor2 protects Pir1 from degradation by the ubiquitin-proteasome system involving the polyubiquitin Ubi4 stress-response protein and the Cul4-Ddb1 E3 ligase. This pathway suppresses widespread and untimely gene expression and is critical for sustaining cell proliferation. Moreover, we find that the dynamic nature of Tor2-mediated control of RNA elimination machinery defines gene expression patterns that coordinate fundamental chromosomal events during gametogenesis, such as meiotic double-strand-break formation and chromosome segregation. These findings have important implications for understanding how the TOR signalling pathway reprogrammes gene expression patterns and contributes to diseases such as cancer.
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23
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Stuparević I, Novačić A, Rahmouni AR, Fernandez A, Lamb N, Primig M. Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev Camb Philos Soc 2021; 96:1092-1113. [PMID: 33599082 DOI: 10.1111/brv.12693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology. However, little is known about the regulatory mechanisms that control the transcription, translation and stability of EXOSC10/Rrp6 during cell growth, development and disease and how these mechanisms evolved from yeast to human. Herein, we provide an overview of the RNA- and protein expression profiles of EXOSC10/Rrp6 during cell division, development and nutritional stress, and we summarize interaction networks and post-translational modifications across species. Additionally, we discuss how known and predicted protein interactions and post-translational modifications influence the stability of EXOSC10/Rrp6. Finally, we explore the idea that different EXOSC10/Rrp6 alleles, which potentially alter cellular protein levels or affect protein function, might influence human development and disease progression. In this review we interpret information from the literature together with genomic data from knowledgebases to inspire future work on the regulation of this essential protein's stability in normal and malignant cells.
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Affiliation(s)
- Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR4301 du CNRS, Orléans, 45071, France
| | - Anne Fernandez
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Ned Lamb
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, 35000, France
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24
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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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25
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Schwer B, Sanchez AM, Shuman S. Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination. RNA (NEW YORK, N.Y.) 2020; 26:1334-1344. [PMID: 32546512 PMCID: PMC7491324 DOI: 10.1261/rna.076463.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/01/2020] [Indexed: 05/08/2023]
Abstract
Fission yeast Erh1 exists in a complex with RNA-binding protein Mmi1. Deletion of erh1 up-regulates the phosphate homeostasis gene pho1, which is normally repressed by transcription in cis of a 5' flanking prt lncRNA. Here we present evidence that de-repression of pho1 by erh1Δ is achieved through precocious 3'-processing/termination of prt lncRNA synthesis, to wit: (i) erh1Δ does not affect the activity of the prt or pho1 promoters per se; (ii) de-repression by erh1Δ depends on CPF (cleavage and polyadenylation factor) subunits Ctf1, Dis2, Ssu72, Swd22, and Ppn1 and on termination factor Rhn1; (iii) de-repression requires synthesis by the Asp1 IPP kinase of inositol 1-pyrophosphates (1-IPPs); (iv) de-repression is effaced by mutating Thr4 of the RNA polymerase II CTD to alanine; and (v) erh1Δ exerts an additive effect on pho1 de-repression in combination with mutating CTD Ser7 to alanine and with deletion of the IPP pyrophosphatase Aps1. These findings point to Erh1 as an antagonist of lncRNA termination in the prt-pho1 axis. In contrast, in mmi1Δ cells there is a reduction in pho1 mRNA and increase in the formation of a prt-pho1 read-through transcript, consistent with Mmi1 being an agonist of prt termination. We envision that Erh1 acts as a brake on Mmi1's ability to promote CPF-dependent termination during prt lncRNA synthesis. Consistent with this idea, erh1Δ de-repression of pho1 was eliminated by mutating the Mmi1-binding sites in the prt lncRNA.
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Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
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26
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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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27
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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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28
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Maxwell PH. Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. Mob DNA 2020; 11:16. [PMID: 32336995 PMCID: PMC7175516 DOI: 10.1186/s13100-020-00215-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogens Candida albicans and Cryptococcus neoformans, and the nonpathogenic species Saccharomyces cerevisiae and Schizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons from Saccharomyces cerevisiae and Tf1 and Tf2 retrotransposons from Schizosaccharomyces pombe to emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
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29
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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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30
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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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31
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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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32
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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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33
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Xu X, Yanagida M. Suppressor screening reveals common kleisin-hinge interaction in condensin and cohesin, but different modes of regulation. Proc Natl Acad Sci U S A 2019; 116:10889-10898. [PMID: 31072933 PMCID: PMC6561158 DOI: 10.1073/pnas.1902699116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cohesin and condensin play fundamental roles in sister chromatid cohesion and chromosome segregation, respectively. Both consist of heterodimeric structural maintenance of chromosomes (SMC) subunits, which possess a head (containing ATPase) and a hinge, intervened by long coiled coils. Non-SMC subunits (Cnd1, Cnd2, and Cnd3 for condensin; Rad21, Psc3, and Mis4 for cohesin) bind to the SMC heads. Here, we report a large number of spontaneous extragenic suppressors for fission yeast condensin and cohesin mutants, and their sites were determined by whole-genome sequencing. Mutants of condensin's non-SMC subunits were rescued by impairing the SUMOylation pathway. Indeed, SUMOylation of Cnd2, Cnd3, and Cut3 occurs in midmitosis, and Cnd3 K870 SUMOylation functionally opposes Cnd subunits. In contrast, cohesin mutants rad21 and psc3 were rescued by loss of the RNA elimination pathway (Erh1, Mmi1, and Red1), and loader mutant mis4 was rescued by loss of Hrp1-mediated chromatin remodeling. In addition, distinct regulations were discovered for condensin and cohesin hinge mutants. Mutations in the N-terminal helix bundle [containing a helix-turn-helix (HTH) motif] of kleisin subunits (Cnd2 and Rad21) rescue virtually identical hinge interface mutations in cohesin and condensin, respectively. These mutations may regulate kleisin's interaction with the coiled coil at the SMC head, thereby revealing a common, but previously unknown, suppression mechanism between the hinge and the kleisin N domain, which is required for successful chromosome segregation. We propose that in both condensin and cohesin, the head (or kleisin) and hinge may interact and collaboratively regulate the resulting coiled coils to hold and release chromosomal DNAs.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, 904-0495 Okinawa, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, 904-0495 Okinawa, Japan
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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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Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- 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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36
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RNA polymerase II CTD interactome with 3' processing and termination factors in fission yeast and its impact on phosphate homeostasis. Proc Natl Acad Sci U S A 2018; 115:E10652-E10661. [PMID: 30355770 DOI: 10.1073/pnas.1810711115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The carboxy-terminal domain (CTD) code encrypted within the Y1S2P3T4S5P6S7 heptad repeats of RNA polymerase II (Pol2) is deeply rooted in eukaryal biology. Key steps to deciphering the code are identifying the events in gene expression that are governed by individual "letters" and then defining a vocabulary of multiletter "words" and their meaning. Thr4 and Ser7 exert opposite effects on the fission yeast pho1 gene, expression of which is repressed under phosphate-replete conditions by transcription of an upstream flanking long noncoding RNA (lncRNA). Here we attribute the derepression of pho1 by a CTD-S7A mutation to precocious termination of lncRNA synthesis, an effect that is erased by mutations of cleavage-polyadenylation factor (CPF) subunits Ctf1, Ssu72, Ppn1, Swd22, and Dis2 and termination factor Rhn1. By contrast, a CTD-T4A mutation hyperrepresses pho1, as do CPF subunit and Rhn1 mutations, implying that T4A reduces lncRNA termination. Moreover, CTD-T4A is synthetically lethal with ppn1∆ and swd22∆, signifying that Thr4 and the Ppn1•Swd22 module play important, functionally redundant roles in promoting Pol2 termination. We find that Ppn1 and Swd22 become essential for viability when the CTD array is curtailed and that S7A overcomes the need for Ppn1•Swd22 in the short CTD context. Mutational synergies highlight redundant essential functions of (i) Ppn1•Swd22 and Rhn1, (ii) Ppn1•Swd22 and Ctf1, and (iii) Ssu72 and Dis2 phosphatases. CTD alleles Y1F, S2A, and T4A have overlapping synthetic lethalities with ppn1∆ and swd22∆, suggesting that Tyr1-Ser2-Thr4 form a three-letter CTD word that abets termination, with Rhn1 being a likely "reader" of this word.
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37
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Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
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Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
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38
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Gallagher PS, Larkin M, Thillainadesan G, Dhakshnamoorthy J, Balachandran V, Xiao H, Wellman C, Chatterjee R, Wheeler D, Grewal SIS. Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control. Nat Struct Mol Biol 2018; 25:372-383. [PMID: 29686279 PMCID: PMC5936480 DOI: 10.1038/s41594-018-0056-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/09/2018] [Indexed: 01/04/2023]
Abstract
Iron metabolism is critical for sustaining life and maintaining human health. Here, we find that iron homeostasis is linked to facultative heterochromatin assembly and regulation of gene expression during adaptive genome control. We show that the fission yeast Clr4/Suv39h histone methyltransferase is part of a rheostat-like mechanism in which transcriptional upregulation of mRNAs in response to environmental change provides feedback to prevent their uncontrolled expression through heterochromatin assembly. Interestingly, proper iron homeostasis is required, as iron depletion or downregulation of iron transporters causes defects in heterochromatin assembly and unrestrained upregulation of gene expression. Remarkably, an unbiased genetic screen revealed that restoration of iron homeostasis is sufficient to re-establish facultative heterochromatin and proper gene control genome-wide. These results establish a role for iron homeostasis in facultative heterochromatin assembly and reveal a dynamic mechanism for reprogramming the genome in response to environmental changes.
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Affiliation(s)
- Pamela S Gallagher
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Wellman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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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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Bresson S, Tollervey D. Surveillance-ready transcription: nuclear RNA decay as a default fate. Open Biol 2018; 8:170270. [PMID: 29563193 PMCID: PMC5881035 DOI: 10.1098/rsob.170270] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic cells synthesize enormous quantities of RNA from diverse classes, most of which are subject to extensive processing. These processes are inherently error-prone, and cells have evolved robust quality control mechanisms to selectively remove aberrant transcripts. These surveillance pathways monitor all aspects of nuclear RNA biogenesis, and in addition remove nonfunctional transcripts arising from spurious transcription and a host of non-protein-coding RNAs (ncRNAs). Surprisingly, this is largely accomplished with only a handful of RNA decay enzymes. It has, therefore, been unclear how these factors efficiently distinguish between functional RNAs and huge numbers of diverse transcripts that must be degraded. Here we describe how bona fide transcripts are specifically protected, particularly by 5' and 3' modifications. Conversely, a plethora of factors associated with the nascent transcripts all act to recruit the RNA quality control, surveillance and degradation machinery. We conclude that initiating RNAPII is 'surveillance ready', with degradation being a default fate for all transcripts that lack specific protective features. We further postulate that this promiscuity is a key feature that allowed the proliferation of vast numbers of ncRNAs in eukaryotes, including humans.
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Affiliation(s)
- Stefan Bresson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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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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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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44
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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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45
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Wittmann S, Renner M, Watts BR, Adams O, Huseyin M, Baejen C, El Omari K, Kilchert C, Heo DH, Kecman T, Cramer P, Grimes JM, Vasiljeva L. The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Nat Commun 2017; 8:14861. [PMID: 28367989 PMCID: PMC5382271 DOI: 10.1038/ncomms14861] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/05/2017] [Indexed: 11/09/2022] Open
Abstract
Termination of RNA polymerase II (Pol II) transcription is an important step in the transcription cycle, which involves the dislodgement of polymerase from DNA, leading to release of a functional transcript. Recent studies have identified the key players required for this process and showed that a common feature of these proteins is a conserved domain that interacts with the phosphorylated C-terminus of Pol II (CTD-interacting domain, CID). However, the mechanism by which transcription termination is achieved is not understood. Using genome-wide methods, here we show that the fission yeast CID-protein Seb1 is essential for termination of protein-coding and non-coding genes through interaction with S2-phosphorylated Pol II and nascent RNA. Furthermore, we present the crystal structures of the Seb1 CTD- and RNA-binding modules. Unexpectedly, the latter reveals an intertwined two-domain arrangement of a canonical RRM and second domain. These results provide important insights into the mechanism underlying eukaryotic transcription termination.
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Affiliation(s)
- Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Max Renner
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Beth R. Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Oliver Adams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Miles Huseyin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Carlo Baejen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Kamel El Omari
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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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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Mukherjee K, Gardin J, Futcher B, Leatherwood J. Relative contributions of the structural and catalytic roles of Rrp6 in exosomal degradation of individual mRNAs. RNA (NEW YORK, N.Y.) 2016; 22:1311-1319. [PMID: 27402898 PMCID: PMC4986887 DOI: 10.1261/rna.051490.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
The RNA exosome is a conserved complex for RNA degradation with two ribonucleolytic subunits, Dis3 and Rrp6. Rrp6 is a 3'-5' exonuclease, but it also has a structural role in helping target RNAs to the Dis3 activity. The relative importance of the exonuclease activity and the targeting activity probably differs between different RNA substrates, but this is poorly understood. To understand the relative contributions of the exonuclease and the targeting activities to the degradation of individual RNA substrates in Schizosaccharomyces pombe, we compared RNA levels in an rrp6 null mutant to those in an rrp6 point mutant specifically defective in exonuclease activity. A wide range of effects was found, with some RNAs dependent mainly on the structural role of Rrp6 ("protein-dependent" targets), other RNAs dependent mainly on the catalytic role ("activity-dependent" targets), and some RNAs dependent on both. Some protein-dependent RNAs contained motifs targeted via the RNA-binding protein Mmi1, while others contained a motif possibly involved in response to iron. In these and other cases Rrp6 may act as a structural adapter to target specific RNAs to the exosome by interacting with sequence-specific RNA-binding proteins.
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Affiliation(s)
- Kaustav Mukherjee
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-5222, USA
| | - Justin Gardin
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-5222, USA
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-5222, USA
| | - Janet Leatherwood
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-5222, USA
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Ukleja M, Valpuesta JM, Dziembowski A, Cuellar J. Beyond the known functions of the CCR4-NOT complex in gene expression regulatory mechanisms: New structural insights to unravel CCR4-NOT mRNA processing machinery. Bioessays 2016; 38:1048-58. [PMID: 27502453 DOI: 10.1002/bies.201600092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large protein assemblies are usually the effectors of major cellular processes. The intricate cell homeostasis network is divided into numerous interconnected pathways, each controlled by a set of protein machines. One of these master regulators is the CCR4-NOT complex, which ultimately controls protein expression levels. This multisubunit complex assembles around a scaffold platform, which enables a wide variety of well-studied functions from mRNA synthesis to transcript decay, as well as other tasks still being identified. Solving the structure of the entire CCR4-NOT complex will help to define the distribution of its functions. The recently published three-dimensional reconstruction of the complex, in combination with the known crystal structures of some of the components, has begun to address this. Methodological improvements in structural biology, especially in cryoelectron microscopy, encourage further structural and protein-protein interaction studies, which will advance our comprehension of the gene expression machinery.
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Affiliation(s)
- Marta Ukleja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland. .,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland. .,Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain. .,Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK.
| | - José María Valpuesta
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Department of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Jorge Cuellar
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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Sugiyama T, Thillainadesan G, Chalamcharla VR, Meng Z, Balachandran V, Dhakshnamoorthy J, Zhou M, Grewal SIS. Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly. Mol Cell 2016; 61:747-759. [PMID: 26942678 DOI: 10.1016/j.molcel.2016.01.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/22/2015] [Accepted: 01/27/2016] [Indexed: 12/21/2022]
Abstract
Erh1, the fission yeast homolog of Enhancer of rudimentary, is implicated in meiotic mRNA elimination during vegetative growth, but its function is poorly understood. We show that Erh1 and the RNA-binding protein Mmi1 form a stoichiometric complex, called the Erh1-Mmi1 complex (EMC), to promote meiotic mRNA decay and facultative heterochromatin assembly. To perform these functions, EMC associates with two distinct complexes, Mtl1-Red1 core (MTREC) and CCR4-NOT. Whereas MTREC facilitates assembly of heterochromatin islands coating meiotic genes silenced by the nuclear exosome, CCR4-NOT promotes RNAi-dependent heterochromatin domain (HOOD) formation at EMC-target loci. CCR4-NOT also assembles HOODs at retrotransposons and regulated genes containing cryptic introns. We find that CCR4-NOT facilitates HOOD assembly through its association with the conserved Pir2/ARS2 protein, and also maintains rDNA integrity and silencing by promoting heterochromatin formation. Our results reveal connections among Erh1, CCR4-NOT, Pir2/ARS2, and RNAi, which target heterochromatin to regulate gene expression and protect genome integrity.
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Affiliation(s)
- Tomoyasu Sugiyama
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Venkata R Chalamcharla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Zhaojing Meng
- Laboratory of Proteomics and Analytical Technologies, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ming Zhou
- Laboratory of Proteomics and Analytical Technologies, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA.
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50
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Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD. The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis. PLoS Genet 2016; 12:e1005817. [PMID: 26828932 PMCID: PMC4735120 DOI: 10.1371/journal.pgen.1005817] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Correct gene expression requires tight RNA quality control both at transcriptional and post-transcriptional levels. Using a splicing-defective allele of PASTICCINO2 (PAS2), a gene essential for plant development, we isolated suppressor mutations modifying pas2-1 mRNA profiles and restoring wild-type growth. Three suppressor of pas2 (sop) mutations modified the degradation of mis-spliced pas2-1 mRNA species, allowing the synthesis of a functional protein. Cloning of the suppressor mutations identified the core subunit of the exosome SOP2/RRP4, the exosome nucleoplasmic cofactor SOP3/HEN2 and a novel zinc-finger protein SOP1 that colocalizes with HEN2 in nucleoplasmic foci. The three SOP proteins counteract post-transcriptional (trans)gene silencing (PTGS), which suggests that they all act in RNA quality control. In addition, sop1 mutants accumulate some, but not all of the misprocessed mRNAs and other types of RNAs that are observed in exosome mutants. Taken together, our data show that SOP1 is a new component of nuclear RNA surveillance that is required for the degradation of a specific subset of nuclear exosome targets.
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Affiliation(s)
- Kian Hématy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- * E-mail:
| | - Yannick Bellec
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States of America
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Pauline Anne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Céline Morineau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Richard P. Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Frederic Beaudoin
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Johnathan A. Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Keithanne Mockaitis
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- Pervasive Technology Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France
| | - Jean-Denis Faure
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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