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Shehzada S, Noto T, Saksouk J, Mochizuki K. A SUMO E3 ligase promotes long non-coding RNA transcription to regulate small RNA-directed DNA elimination. eLife 2024; 13:e95337. [PMID: 38197489 PMCID: PMC10830130 DOI: 10.7554/elife.95337] [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: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNAs (scnRNAs) and the nascent lncRNA transcripts from the somatic genome has been proposed to induce target-directed small RNA degradation (TDSD), and scnRNAs not targeted for TDSD later target the germline-limited sequences for programmed DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from the somatic genome and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II with chromatin. These results suggest that Ema2-directed SUMOylation actively promotes lncRNA transcription, which is a prerequisite for communication between the genome and small RNAs.
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Affiliation(s)
- Salman Shehzada
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Tomoko Noto
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
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Tian M, Cai X, Liu Y, Liucong M, Howard-Till R. A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:595-608. [PMID: 37078080 PMCID: PMC10077211 DOI: 10.1007/s42995-022-00149-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/28/2022] [Indexed: 05/03/2023]
Abstract
Meiosis is a critical cell division program that produces haploid gametes for sexual reproduction. Abnormalities in meiosis are often causes of infertility and birth defects (e.g., Down syndrome). Most organisms use a highly specialized zipper-like protein complex, the synaptonemal complex (SC), to guide and stabilize pairing of homologous chromosomes in meiosis. Although the SC is critical for meiosis in many eukaryotes, there are organisms that perform meiosis without a functional SC. However, such SC-less meiosis is poorly characterized. To understand the features of SC-less meiosis and its adaptive significance, the ciliated protozoan Tetrahymena was selected as a model. Meiosis research in Tetrahymena has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis, yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of SC. Here, aiming at promoting a wider application of Tetrahymena for meiosis research, we introduce basic concepts and core techniques for studying meiosis in Tetrahymena and then suggest future directions for expanding the current Tetrahymena meiosis research toolbox. These methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel features. Such data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00149-8.
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Affiliation(s)
- Miao Tian
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Institute of Human Genetics, CNRS, University of Montpellier, 34090 Montpellier, France
| | - Xia Cai
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yujie Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Mingmei Liucong
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Rachel Howard-Till
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA USA
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Zhang J, Tian M, Chen K, Yan G, Xiong J, Miao W. Zfp1, a Cys2His2 zinc finger protein is required for meiosis initiation in Tetrahymena thermophila. Cell Cycle 2022; 21:1422-1433. [PMID: 35293272 PMCID: PMC9345619 DOI: 10.1080/15384101.2022.2053449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Meiosis is an important and highly conserved process that occurs during eukaryotic sexual reproduction. Diverse mechanisms are responsible for meiosis initiation among eukaryotes, and transcription factors have been established to have an important role in many species. However, the specific function of transcription factors in initiating meiosis in ciliates is unknown. Here we show that a putative Cys2His2 zinc finger-containing transcription factor encoded by the ZFP1 gene is specifically expressed during sexual reproduction in Tetrahymena thermophila. Meiosis is not initiated in the cells lacking ZFP1. Transcriptome sequencing analyses reveal that Zfp1 is required for the expression of many meiosis-specific genes. Our results indicate that Zfp1 could be a transcriptional activator required for meiosis initiation in T. thermophila.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Miao Tian
- Department of Chromosome Biology and Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, Shanghai, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China.,CAS Center for Excellence in Animal Evolution and Genetics, Kunming, Yunnan, China
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4
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Broad domains of histone marks in the highly compact Paramecium macronuclear genome. Genome Res 2022; 32:710-725. [PMID: 35264449 PMCID: PMC8997361 DOI: 10.1101/gr.276126.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
Abstract
The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.
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Identification and utilization of a mutated 60S ribosomal subunit coding gene as an effective and cost-efficient selection marker for Tetrahymena genetic manipulation. Int J Biol Macromol 2022; 204:1-8. [PMID: 35122796 DOI: 10.1016/j.ijbiomac.2022.01.188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 01/05/2023]
Abstract
Since the onset of molecular biology, the ciliate Tetrahymena thermophila has been one of the most convenient single-celled model eukaryotes for genetics, biochemistry, and cell biology. Particularly, thanks to the availability of several different selection markers, it is possible to knock out or knock in genes at multiple genetic loci simultaneously in Tetrahymena, which makes it an excellent model ciliate for tackling complex regulatory mechanisms. Despite these selection markers are efficient for genetic manipulation, the costly drugs used for selection have highlighted the urgent demand for an additional cost-efficient and effective selection marker. Here, we found that a mutated 60S ribosomal subunit component, RPL36A, confers T. thermophila with cycloheximide resistance. On top of that, we developed a cycloheximide cassette and explored suitable transformation and selection conditions. Using the new cassette, we obtained both knockout and knock-in strains successfully at a relatively low cost. This study also provided the first evidence that a cycloheximide resistance gene can be engineered as a selection marker to completely delete a gene from the highly-polyploid somatic nucleus in Tetrahymena.
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Allen SE, Nowacki M. Roles of Noncoding RNAs in Ciliate Genome Architecture. J Mol Biol 2020; 432:4186-4198. [PMID: 31926952 PMCID: PMC7374600 DOI: 10.1016/j.jmb.2019.12.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
Ciliates are an interesting model system for investigating diverse functions of noncoding RNAs, especially in genome defence pathways. During sexual development, the ciliate somatic genome undergoes massive rearrangement and reduction through removal of transposable elements and other repetitive DNA. This is guided by a multitude of noncoding RNAs of different sizes and functions, the extent of which is only recently becoming clear. The genome rearrangement pathways evolved as a defence against parasitic DNA, but interestingly also use the transposable elements and transposases to execute their own removal. Thus, ciliates are also a good model for the coevolution of host and transposable element, and the mutual dependence between the two. In this review, we summarise the genome rearrangement pathways in three diverse species of ciliate, with focus on recent discoveries and the roles of noncoding RNAs. Ciliate genomes undergo massive rearrangement and reduction during development. Transposon elimination is guided by small RNAs and carried out by transposases. New pathways for noncoding RNA production have recently been discovered in ciliates. Diverse ciliate species have different mechanisms for RNA-guided genome remodeling.
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Affiliation(s)
- Sarah E Allen
- Institute of Cell Biology, University of Bern, Switzerland
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Abstract
Mediator is a large, multi-module complex that plays a key role in transcription regulation in eukaryotes. A divergent Mediator from a unicellular eukaryote has been identified and characterized, revealing novel adaptations to mRNA and ncRNA transcription.
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Affiliation(s)
- Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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