1
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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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2
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Su Y, Wu J, Chen W, Shan J, Chen D, Zhu G, Ge S, Liu Y. Spliceosomal snRNAs, the Essential Players in pre-mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics. Adv Biol (Weinh) 2024:e2400006. [PMID: 38797893 DOI: 10.1002/adbi.202400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non-coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre-mRNAs). They are transcribed by DNA-dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3' end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre-mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue-specific regulation of snRNAs.
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Affiliation(s)
- Yuan Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Junling Shan
- Department of basic medicine, Guangxi Medical University of Nursing College, Nanning, Guangxi, 530021, China
| | - Dan Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, 530011, China
| | - Guangyu Zhu
- Guangxi Medical University Hospital of Stomatology, Nanning, Guangxi, 530021, China
| | - Shengchao Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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3
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Ma T, Xiong ES, Lardelli RM, Lykke-Andersen J. Sm complex assembly and 5' cap trimethylation promote selective processing of snRNAs by the 3' exonuclease TOE1. Proc Natl Acad Sci U S A 2024; 121:e2315259121. [PMID: 38194449 PMCID: PMC10801842 DOI: 10.1073/pnas.2315259121] [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: 09/01/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024] Open
Abstract
Competing exonucleases that promote 3' end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3' exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity toward canonical snRNAs through their Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
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Affiliation(s)
- Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Erica S. Xiong
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Rea M. Lardelli
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
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4
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Peng Q, Wang Y, Xiao Y, Chang H, Luo S, Wang D, Rong YS. Drosophila Amus and Bin3 methylases functionally replace mammalian MePCE for capping and the stabilization of U6 and 7SK snRNAs. SCIENCE ADVANCES 2023; 9:eadj9359. [PMID: 38100593 PMCID: PMC10848712 DOI: 10.1126/sciadv.adj9359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
U6 and 7SK snRNAs have a 5' cap, believed to be essential for their stability and maintained by mammalian MePCE or Drosophila Bin3 enzymes. Although both proteins are required for 7SK stability, loss of neither destabilizes U6, casting doubts on the function of capping U6. Here, we show that the Drosophila Amus protein, homologous to both proteins, is essential for U6 but not 7SK stability. The loss of U6 is rescued by the expression of an Amus-MePCE hybrid protein harboring the methyltransferase domain from MePCE, highlighting the conserved function of the two proteins as the U6 capping enzyme. Our investigations in human cells establish a dependence of both U6 and 7SK stability on MePCE, resolving a long-standing uncertainty. While uncovering a division of labor of Bin3/MePCE/Amus proteins, we found a "Bin3-Box" domain present only in enzymes associated with 7SK regulation. Targeted mutagenesis confirms its importance for Bin3 function, revealing a possible conserved element in 7SK but not U6 biology.
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Affiliation(s)
- Qiu Peng
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yiqing Wang
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
| | - Ying Xiao
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
| | - Hua Chang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shishi Luo
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
| | - Danling Wang
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yikang S. Rong
- MOE Key Lab of Rare Pediatric Diseases, Hengyang College of Medicine, University of South China, Hengyang, China
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5
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Siena LA, Michaud C, Selles B, Vega JM, Pessino SC, Ingouff M, Ortiz JPA, Leblanc O. TRIMETHYLGUANOSINE SYNTHASE1 mutations decanalize female germline development in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:597-612. [PMID: 37548040 DOI: 10.1111/nph.19179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023]
Abstract
Here, we report the characterization of a plant RNA methyltransferase, orthologous to yeast trimethylguanosine synthase1 (Tgs1p) and whose downregulation was associated with apomixis in Paspalum grasses. Using phylogenetic analyses and yeast complementation, we determined that land plant genomes all encode a conserved, specific TGS1 protein. Next, we studied the role of TGS1 in female reproduction using reporter lines and loss-of-function mutants in Arabidopsis thaliana. pAtTGS1:AtTGS1 reporters showed a dynamic expression pattern. They were highly active in the placenta and ovule primordia at emergence but, subsequently, showed weak signals in the nucellus. Although expressed throughout gametophyte development, activity became restricted to the female gamete and was also detected after fertilization during embryogenesis. TGS1 depletion altered the specification of the precursor cells that give rise to the female gametophytic generation and to the sporophyte, resulting in the formation of a functional aposporous-like lineage. Our results indicate that TGS1 participates in the mechanisms restricting cell fate acquisition to a single cell at critical transitions throughout the female reproductive lineage and, thus, expand our current knowledge of the mechanisms governing female reproductive fate in plants.
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Affiliation(s)
- Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | | | - Benjamin Selles
- DIADE, Univ Montpellier, IRD, CIRAD, 34394, Montpellier, France
| | - Juan Manuel Vega
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Mathieu Ingouff
- DIADE, Univ Montpellier, IRD, CIRAD, 34394, Montpellier, France
| | - Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Olivier Leblanc
- DIADE, Univ Montpellier, IRD, CIRAD, 34394, Montpellier, France
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6
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Ma T, Xiong ES, Lardelli RM, Lykke-Andersen J. The 3' exonuclease TOE1 selectively processes snRNAs through recognition of Sm complex assembly and 5' cap trimethylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553431. [PMID: 37645788 PMCID: PMC10462049 DOI: 10.1101/2023.08.15.553431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Competing exonucleases that promote 3' end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3' exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity towards canonical snRNAs by recognizing Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
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Affiliation(s)
- Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erica S Xiong
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rea M Lardelli
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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7
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Chen L, Roake CM, Maccallini P, Bavasso F, Dehghannasiri R, Santonicola P, Mendoza-Ferreira N, Scatolini L, Rizzuti L, Esposito A, Gallotta I, Francia S, Cacchione S, Galati A, Palumbo V, Kobin MA, Tartaglia G, Colantoni A, Proietti G, Wu Y, Hammerschmidt M, De Pittà C, Sales G, Salzman J, Pellizzoni L, Wirth B, Di Schiavi E, Gatti M, Artandi S, Raffa GD. TGS1 impacts snRNA 3'-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration. Nucleic Acids Res 2022; 50:12400-12424. [PMID: 35947650 PMCID: PMC9757054 DOI: 10.1093/nar/gkac659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5'-monomethylguanosine cap of small nuclear RNAs (snRNAs) to a trimethylguanosine cap. Here, we show that loss of TGS1 in Caenorhabditis elegans, Drosophila melanogaster and Danio rerio results in neurological phenotypes similar to those caused by survival motor neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3' tails that are often uridylated. snRNAs with defective 3' terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.
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Affiliation(s)
- Lu Chen
- Correspondence may also be addressed to Lu Chen.
| | | | - Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Natalia Mendoza-Ferreira
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Ludovico Rizzuti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | | | - Ivan Gallotta
- Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Sofia Francia
- IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy,Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Valeria Palumbo
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Marie A Kobin
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Gian Gaetano Tartaglia
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Alessio Colantoni
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Gabriele Proietti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Yunming Wu
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthias Hammerschmidt
- Institute for Zoology, Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | | | - Gabriele Sales
- Department of Biology, University of Padova, Padua, Italy
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Columbia University, NY 10032, USA,Department of Pathology and Cell Biology, Columbia University, NY 10032, USA,Department of Neurology, Columbia University, NY 10032, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany,Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, IBBR, CNR, Naples, Italy,Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Rome, Italy
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8
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Spotting the Targets of the Apospory Controller TGS1 in Paspalum notatum. PLANTS 2022; 11:plants11151929. [PMID: 35893633 PMCID: PMC9332697 DOI: 10.3390/plants11151929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
Sexuality and apomixis are interconnected plant reproductive routes possibly behaving as polyphenic traits under the influence of the environment. In the subtropical grass Paspalum notatum, one of the controllers of apospory, a main component of gametophytic apomixis reproduction, is TRIMETHYLGUANOSINE SYNTHASE 1 (TGS1), a multifunctional gene previously associated with RNA cleavage regulation (including mRNA splicing as well as rRNA and miRNA processing), transcriptional modulation and the establishment of heterochromatin. In particular, the downregulation of TGS1 induces a sexuality decline and the emergence of aposporous-like embryo sacs. The present work was aimed at identifying TGS1 target RNAs expressed during reproductive development of Paspalum notatum. First, we mined available RNA databases originated from spikelets of sexual and apomictic plants, which naturally display a contrasting TGS1 representation, to identify differentially expressed mRNA splice variants and miRNAs. Then, the role of TGS1 in the generation of these particular molecules was investigated in antisense tgs1 sexual lines. We found that CHLOROPHYLL A-B BINDING PROTEIN 1B-21 (LHC Ib-21, a component of the chloroplast light harvesting complex), QUI-GON JINN (QGJ, encoding a MAP3K previously associated with apomixis) and miR2275 (a meiotic 24-nt phasi-RNAs producer) are directly or indirectly targeted by TGS1. Our results point to a coordinated control exercised by signal transduction and siRNA machineries to induce the transition from sexuality to apomixis.
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9
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Li X, Peng J, Yi C. The epitranscriptome of small non-coding RNAs. Noncoding RNA Res 2021; 6:167-173. [PMID: 34820590 PMCID: PMC8581453 DOI: 10.1016/j.ncrna.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.
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Affiliation(s)
- Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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10
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Sandhu R, Sinha A, Montpetit B. The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae. Nucleic Acids Res 2021; 49:2552-2568. [PMID: 33577675 PMCID: PMC7969001 DOI: 10.1093/nar/gkab071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/30/2023] Open
Abstract
The meiotic gene expression program in Saccharomyces cerevisiae involves regulated splicing of meiosis-specific genes via multiple splicing activators (e.g. Mer1, Nam8, Tgs1). Here, we show that the SR protein Npl3 is required for meiotic splicing regulation and is essential for proper execution of the meiotic cell cycle. The loss of Npl3, though not required for viability in mitosis, caused intron retention in meiosis-specific transcripts, inefficient meiotic double strand break processing and an arrest of the meiotic cell cycle. The targets of Npl3 overlapped in some cases with other splicing regulators, while also having unique target transcripts that were not shared. In the absence of Npl3, splicing defects for three transcripts (MER2, HOP2 and SAE3) were rescued by conversion of non-consensus splice sites to the consensus sequence. Methylation of Npl3 was further found to be required for splicing Mer1-dependent transcripts, indicating transcript-specific mechanisms by which Npl3 supports splicing. Together these data identify an essential function for the budding yeast SR protein Npl3 in meiosis as part of the meiotic splicing regulatory network.
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Affiliation(s)
- Rima Sandhu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Aniketa Sinha
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
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11
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Yu H, Tsuchida M, Ando M, Hashizaki T, Shimada A, Takahata S, Murakami Y. Trimethylguanosine synthase 1 (Tgs1) is involved in Swi6/HP1-independent siRNA production and establishment of heterochromatin in fission yeast. Genes Cells 2021; 26:203-218. [PMID: 33527595 DOI: 10.1111/gtc.12833] [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: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/27/2022]
Abstract
In fission yeast, siRNA generated by RNA interference (RNAi) factors plays critical roles in establishment and maintenance of heterochromatin. To achieve efficient siRNA synthesis, RNAi factors assemble on heterochromatin via association with Swi6, a homologue of heterochromatin protein 1 (HP1), and heterochromatic noncoding RNA (hncRNA) retained on chromatin. In addition, spliceosomes formed on hncRNA introns recruit RNAi factors to hncRNA and heterochromatin. Small nuclear RNAs, components of the spliceosome, have a trimethylguanosine (TMG) cap that is generated by Tgs1-dependent hypermethylation of the normal m7G cap; this cap is required for efficient splicing of some mRNAs in budding yeast and Drosophila. In this study, we found that loss of Tgs1 in fission yeast destabilizes centromeric heterochromatin. Tgs1 was required for Swi6-independent siRNA synthesis, as well as for the establishment of centromeric heterochromatin. Loss of Tgs1 affected the splicing efficiency of hncRNA introns in the absence of Swi6. Furthermore, some hncRNAs have a TMG cap, and we found that loss of Tgs1 diminished the chromatin binding of these hncRNAs. Together, these results suggest that the Tgs1-dependent TMG cap plays critical roles in establishment of heterochromatin by ensuring spliceosome-dependent recruitment of RNAi factors and regulating the binding between chromatin and hncRNA.
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Affiliation(s)
- Hiroki Yu
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Ambitious Leader's Program Fostering Future Leaders to Open New Frontiers in Materials Science (ALP), Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mai Tsuchida
- Laboratory for Cell Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Motoyoshi Ando
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Tomoka Hashizaki
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Atsushi Shimada
- Laboratory for Cell Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shinya Takahata
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yota Murakami
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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