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Chen Z, Li J, Salas-Leiva DE, Chen M, Chen S, Li S, Wu Y, Yi Z. Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:609-623. [PMID: 37078085 PMCID: PMC10077286 DOI: 10.1007/s42995-022-00147-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/23/2022] [Indexed: 05/03/2023]
Abstract
Adaptations of ciliates to hypoxic environments have arisen independently several times. Studies on mitochondrion-related organelle (MRO) metabolisms from distinct anaerobic ciliate groups provide evidence for understanding the transitions from mitochondria to MROs within eukaryotes. To deepen our knowledge about the evolutionary patterns of ciliate anaerobiosis, mass-culture and single-cell transcriptomes of two anaerobic species, Metopus laminarius (class Armophorea) and Plagiopyla cf. narasimhamurtii (class Plagiopylea), were sequenced and their MRO metabolic maps were compared. In addition, we carried out comparisons using publicly available predicted MRO proteomes from other ciliate classes (i.e., Armophorea, Litostomatea, Muranotrichea, Oligohymenophorea, Parablepharismea and Plagiopylea). We found that single-cell transcriptomes were similarly comparable to their mass-culture counterparts in predicting MRO metabolic pathways of ciliates. The patterns of the components of the MRO metabolic pathways might be divergent among anaerobic ciliates, even among closely related species. Notably, our findings indicate the existence of group-specific functional relics of electron transport chains (ETCs). Detailed group-specific ETC functional patterns are as follows: full oxidative phosphorylation in Oligohymenophorea and Muranotrichea; only electron-transfer machinery in Armophorea; either of these functional types in Parablepharismea; and ETC functional absence in Litostomatea and Plagiopylea. These findings suggest that adaptation of ciliates to anaerobic conditions is group-specific and has occurred multiple times. Our results also show the potential and the limitations of detecting ciliate MRO proteins using single-cell transcriptomes and improve the understanding of the multiple transitions from mitochondria to MROs within ciliates. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00147-w.
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Affiliation(s)
- Zhicheng Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | | | - Miaoying Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Shilong Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Senru Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Yanyan Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
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2
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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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3
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Case Study of the Response of N 6-Methyladenine DNA Modification to Environmental Stressors in the Unicellular Eukaryote Tetrahymena thermophila. mSphere 2021; 6:e0120820. [PMID: 34047647 PMCID: PMC8265677 DOI: 10.1128/msphere.01208-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Rediscovered as a potential epigenetic mark, N6-methyladenine DNA modification (6mA) was recently reported to be sensitive to environmental stressors in several multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. Here, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Single-molecule, real-time (SMRT) sequencing reveals that DNA 6mA levels in starved cells are significantly reduced, especially symmetric 6mA, compared to those in vegetatively growing cells. Despite a global 6mA reduction, the fraction of asymmetric 6mA with a high methylation level was increased, which might be the driving force for stronger nucleosome positioning in starved cells. Starvation affects expression of many metabolism-related genes, the expression level change of which is associated with the amount of 6mA change, thereby linking 6mA with global transcription and starvation adaptation. The reduction of symmetric 6mA and the increase of asymmetric 6mA coincide with the downregulation of AMT1 and upregulation of AMT2 and AMT5, which are supposedly the MT-A70 methyltransferases required for symmetric and asymmetric 6mA, respectively. These results demonstrated that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes. IMPORTANCE Increasing evidence indicated that 6mA could respond to environmental stressors in multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. In the present work, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Our results provide insights into how Tetrahymena fine-tunes its 6mA level and composition upon starvation, suggesting that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes.
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4
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New contribution to epigenetic studies: Isolation of micronuclei with high purity and DNA integrity in the model ciliated protist, Tetrahymena thermophila. Eur J Protistol 2021; 80:125804. [PMID: 34062315 DOI: 10.1016/j.ejop.2021.125804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 10/24/2022]
Abstract
The ciliated protist Tetrahymena thermophila is a well-known model organism with typical nuclear dimorphism containing a somatic macronucleus (MAC) and a germline micronucleus (MIC). The presence in the same cell compartment of two nuclei with distinctly different structural and functional properties provides an ideal model system to explore mechanisms of genome maintenance. Although methods for the isolation of MIC have been available for many years, cross-contamination and DNA degradation remain unresolved. Here, we describe a reliable and quick method to isolate MIC with high purity and DNA integrity in T. thermophila. Different factors are examined to optimize the MIC purification. The MAC contamination ratio in purified MIC is about 0.19% and DNA integrity of purified MIC is maintained. We also establish a more accurate method to detect the contamination rate of nuclei including microscopic observation and PCR detection. This study will facilitate further epigenetic research in Tetrahymena.
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5
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Liu Y, Nan B, Niu J, Kapler GM, Gao S. An Optimized and Versatile Counter-Flow Centrifugal Elutriation Workflow to Obtain Synchronized Eukaryotic Cells. Front Cell Dev Biol 2021; 9:664418. [PMID: 33959616 PMCID: PMC8093812 DOI: 10.3389/fcell.2021.664418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/23/2021] [Indexed: 11/21/2022] Open
Abstract
Cell synchronization is a powerful tool to understand cell cycle events and its regulatory mechanisms. Counter-flow centrifugal elutriation (CCE) is a more generally desirable method to synchronize cells because it does not significantly alter cell behavior and/or cell cycle progression, however, adjusting specific parameters in a cell type/equipment-dependent manner can be challenging. In this paper, we used the unicellular eukaryotic model organism, Tetrahymena thermophila as a testing system for optimizing CCE workflow. Firstly, flow cytometry conditions were identified that reduced nuclei adhesion and improved the assessment of cell cycle stage. We then systematically examined how to achieve the optimal conditions for three critical factors affecting the outcome of CCE, including loading flow rate, collection flow rate and collection volume. Using our optimized workflow, we obtained a large population of highly synchronous G1-phase Tetrahymena as measured by 5-ethynyl-2'-deoxyuridine (EdU) incorporation into nascent DNA strands, bulk DNA content changes by flow cytometry, and cell cycle progression by light microscopy. This detailed protocol can be easily adapted to synchronize other eukaryotic cells.
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Affiliation(s)
- Yongqiang Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bei Nan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Junhua Niu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Geoffrey M. Kapler
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Further insights into the phylogeny of peniculid ciliates (Ciliophora, Oligohymenophorea) based on multigene data. Mol Phylogenet Evol 2020; 154:107003. [PMID: 33137410 DOI: 10.1016/j.ympev.2020.107003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
Peniculids comprise a large order of ciliated protists in Class Oligohymenophorea having many unresolved evolutionary relationships. Herein, we report 27 new sequences, including 18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA and the mitochondrial cox1 genes of eight peniculids. We conducted phylogenetic analyses based on each these markers and on a four-gene concatenated data set (18S rRNA, ITS1-5.8S- ITS2 rRNA, 28S rRNA, and cox1 gene). The main findings are: 1) subclass Peniculia and family Parameciidae are monophyletic, with genus Frontonia remaining non-monophyletic; 2) Urocentrids have traditionally been regarded as a family, multi-gene analyses support the rank of Urocentrida and consistently recovers this order as sister to Peniculida, and Urocentrida and Peniculida comprise subclass Peniculia in agreement with Lynn's (2008) classification; 3) discrepancies between multiple-gene phylogenies, and conflicts with morphologic data regarding genus Frontonia necessitate expansion and revision of species diagnoses and we propose consideration of Group III of Frontonia (including F. didieri, F. ocularis, F. anatolica, F. pusilla and F. elegans) as incertae sedis in Peniculida; 4) multi-gene analyses of Parameciidae support five previously established subgenera. Paramecium buetschlii is placed in subgenus Chloroparamecium, and P. chlorelligerum into subgenus Viridoparamecium.
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7
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Wang Y, Sheng Y, Liu Y, Zhang W, Cheng T, Duan L, Pan B, Qiao Y, Liu Y, Gao S. A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription. Nucleic Acids Res 2020; 47:11771-11789. [PMID: 31722409 PMCID: PMC7145601 DOI: 10.1093/nar/gkz1053] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Rediscovered as a potential eukaryotic epigenetic mark, DNA N6-adenine methylation (6mA) varies across species in abundance and its relationships with transcription. Here we characterize AMT1—representing a distinct MT-A70 family methyltransferase—in the ciliate Tetrahymena thermophila. AMT1 loss-of-function leads to severe defects in growth and development. Single Molecule, Real-Time (SMRT) sequencing reveals that AMT1 is required for the bulk of 6mA and all symmetric methylation at the ApT dinucleotides. The detection of hemi-methylated ApT sites suggests a semi-conservative mechanism for maintaining symmetric methylation. AMT1 affects expression of many genes; in particular, RAB46, encoding a Rab family GTPase involved in contractile vacuole function, is likely a direct target. The distribution of 6mA resembles H3K4 methylation and H2A.Z, two conserved epigenetic marks associated with RNA polymerase II transcription. Furthermore, strong 6mA and nucleosome positioning in wild-type cells is attenuated in ΔAMT1 cells. Our results support that AMT1-catalyzed 6mA is an integral part of the transcription-associated epigenetic landscape. AMT1 homologues are generally found in protists and basal fungi featuring ApT hyper-methylation associated with transcription, which are missing in animals, plants, and true fungi. This dichotomy of 6mA functions and the underlying molecular mechanisms may have implications in eukaryotic diversification.
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Affiliation(s)
- Yuanyuan Wang
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yalan Sheng
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yongqiang 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wenxin Zhang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Ting Cheng
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lili Duan
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Pan
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yu Qiao
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shan Gao
- 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 266003, China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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8
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The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1534-1542. [PMID: 32297047 DOI: 10.1007/s11427-020-1689-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/26/2020] [Indexed: 01/03/2023]
Abstract
The ciliate Tetrahymena thermophila has been a powerful model system for molecular and cellular biology. However, some investigations have been limited due to the incomplete closure and sequencing of the macronuclear genome assembly, which for many years has been stalled at 1,158 scaffolds, with large sections of unknown sequences (available in Tetrahymena Genome Database, TGD, http://ciliate.org/ ). Here we completed the first chromosome-level Tetrahymena macronuclear genome assembly, with approximately 300× long Single Molecule, Real-Time reads of the wild-type SB210 cells-the reference strain for the initial macronuclear genome sequencing project. All 181 chromosomes were capped with two telomeres and gaps were entirely closed. The completed genome shows significant improvements over the current assembly (TGD 2014) in both chromosome structure and sequence integrity. The majority of previously identified gene models shown in TGD were retained, with the addition of 36 new genes and 883 genes with modified gene models. The new genome and annotation were incorporated into TGD. This new genome allows for pursuit in some underexplored areas that were far more challenging previously; two of them, genome scrambling and chromosomal copy number, were investigated in this study. We expect that the completed macronuclear genome will facilitate many studies in Tetrahymena biology, as well as multiple lines of research in other eukaryotes.
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9
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Wang C, Yan Y, Chen X, Al‐Farraj SA, El‐Serehy HA, Gao F. Further analyses on the evolutionary “key‐protist”
Halteria
(Protista, Ciliophora) based on transcriptomic data. ZOOL SCR 2019. [DOI: 10.1111/zsc.12380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chundi Wang
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
- Department of Genetics and Development Columbia University Medical Center New York NY USA
| | - Saleh A. Al‐Farraj
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Hamed A. El‐Serehy
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
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10
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Xu J, Li X, Song W, Wang W, Gao S. Cyclin Cyc2p is required for micronuclear bouquet formation in Tetrahymena thermophila. SCIENCE CHINA-LIFE SCIENCES 2019; 62:668-680. [PMID: 30820856 DOI: 10.1007/s11427-018-9369-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/19/2018] [Indexed: 01/31/2023]
Abstract
Meiotic bouquet formation (known as crescent formation in Tetrahymena thermophila) is indispensable for homologous pairing and recombination, but the regulatory mechanism of bouquet formation remains largely unknown. As a conjugation specific cyclin gene, CYC2 knockout mutants failed to form an elongated crescent structure and aborted meiosis progress in T. thermophila. γ-H2A.X staining revealed fewer micronuclear DNA double-strand breaks (DSBs) in cyc2Δ cells than in wild-type cells. Furthermore, cyc2Δ cells still failed to form a crescent structure even though DSBs were induced by exogenous agents, indicating that a lack of DSBs was not completely responsible for failure to enter the crescent stage. Tubulin staining showed that impaired perinuclear microtubule structure may contribute to the blockage in micronuclear elongation. At the same time, expression of microtubule-associated kinesin genes, KIN11 and KIN141, was significantly downregulated in cyc2Δ cells. Moreover, micronuclear specific accumulation of heterochromatin marker trimethylated H3K23 abnormally increased in the cyc2Δ mutants. Together, these results show that cyclin Cyc2p is required for micronuclear bouquet formation via controlling microtubule-directed nuclear elongation in Tetrahymena.
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Affiliation(s)
- Jing Xu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- College of Life Science, Shanxi University, Taiyuan, 030006, China
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Xiaoxiong Li
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Weibo Song
- 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, 266003, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China.
| | - Shan Gao
- 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, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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11
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Wang Y, Wang C, Jiang Y, Katz LA, Gao F, Yan Y. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. SCIENCE CHINA-LIFE SCIENCES 2019; 62:203-214. [PMID: 30671886 DOI: 10.1007/s11427-018-9422-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/06/2018] [Indexed: 11/26/2022]
Abstract
Sequence-based approaches, such as analyses of ribosome DNA (rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities. However, recent studies demonstrate both rDNA copy number variation and intra-individual (intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA (SSU rDNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that: (i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa; (ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template; (iii) compared with the most common version, other variant sequences differ in only 1-3 nucleotides, likely generated during macronuclear (somatic) amplification; (iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses; (v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall, these analyses indicate the need for careful consideration of SSU rDNA variation in analyses of the role of ciliates in ecosystems.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA.
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12
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Sheng Y, He M, Zhao F, Shao C, Miao M. Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti. Mol Phylogenet Evol 2018; 129:338-345. [DOI: 10.1016/j.ympev.2018.06.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022]
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13
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Pan M, Wang Y, Yin H, Pan X, Mu W, Al-Rasheid KAS, Fan X, Pan X. Redescription of a Hymenostome Ciliate, Tetrahymena setosa (Protozoa, Ciliophora) Notes on its Molecular Phylogeny. J Eukaryot Microbiol 2018; 66:413-423. [PMID: 30099801 DOI: 10.1111/jeu.12683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/25/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Abstract
In recent years, Tetrahymena species have been used as model organisms for research in a wide range of fields, highlighting the need for a fuller understanding of the taxonomy of this group. It is in this context that this paper uses living observation and silver staining methods to investigate the morphology and infraciliature of one Tetrahymena species, T. setosa (Schewiakoff 1892 Verh. Naturh. Med. Ver. Heidelb., 4:544) McCoy (1975) Acta Protozool., 14:253; the senior subjective synonym of T. setifera Holz and Corliss (1956) J. Protozool., 3:112; isolated from a freshwater pond in Harbin, north-eastern China. This organism can be distinguished from other described Tetrahymena species mainly by its single caudal cilium, which is about twice the length of the somatic ciliature. While the Harbin isolate appears similar to the population described by Holz and Corliss (1956) J. Protozool., 3:112, an improved diagnosis for T. setosa is given based on the previous descriptions and the Harbin population. In summary, this species can be recognized mainly by the combination of the following characters: body in vivo approximately 40 μm × 25 μm, 21-26 somatic kineties, one to four contractile vacuole pores associated with meridians 6-11 and a single caudal cilium. The small subunit ribosomal (SSU) rRNA gene and the cox1 gene sequences of Harbin population are also characterized in order to corroborate that the isolated species branches in phylogenetic trees as a T. setosa species. The phylogenetic analysis also indicated that sequences of populations of Tetrahymena species should be published with detailed morphological identifications.
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Affiliation(s)
- Mengmeng Pan
- College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Haiwei Yin
- College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Xuyue Pan
- The Third Affiliated Hospital of Beijing University of Traditional Chinese Medicine, Beijing, 100078, China
| | - Weijie Mu
- College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xuming Pan
- College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
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Zhang T, Wang C, Katz LA, Gao F. A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora). SCIENCE CHINA-LIFE SCIENCES 2018; 61:1071-1078. [DOI: 10.1007/s11427-018-9333-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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15
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Song W, Wang L, Li L, Al-Farraj SA, Aleidan A, Smith S, Hu X. Morphological Characterizations of Four Species of Parallelostrombidium
(Ciliophora, Oligotrichia), with a Note on the Phylogeny of the Genus. J Eukaryot Microbiol 2018; 65:679-693. [DOI: 10.1111/jeu.12513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/07/2018] [Accepted: 02/12/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Wen Song
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Lun Wang
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Lifang Li
- Marine College; Shandong University; Weihai 264209 China
| | - Saleh A. Al-Farraj
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - Abdullah Aleidan
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - Susan Smith
- Department of Marine Science; University of Connecticut; Groton Connecticut 06340 USA
| | - Xiaozhong Hu
- Laboratory of Protozoology; Institute of Evolution and Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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16
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Yan Y, Fan Y, Luo X, El-Serehy HA, Bourland W, Chen X. New contribution to the species-rich genus Euplotes: Morphology, ontogeny and systematic position of two species (Ciliophora; Euplotia). Eur J Protistol 2018; 64:20-39. [PMID: 29621653 DOI: 10.1016/j.ejop.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
Abstract
The morphology, ontogeny and phylogeny of two Euplotes species, E. estuarinus sp. nov. and a population of E. platystoma Dragesco and Dragesco-Kernéis, 1986, both collected from tropical brackish waters in south China, were investigated based on living morphology, ciliary pattern and molecular data. Euplotes estuarinus sp. nov. is small (about 60 × 40 μm in vivo), has a dargyrome of the double-eurystomus type, and the transverse cirri are arranged in two groups, with two left and three right ones. The original description of the poorly known species, E. platystoma, is brief, and the species was never investigated using live observation and molecular methods Hence, we provided a detailed redescription. Some stages of their morphogenesis were observed which proceed in the same pattern as in their congeners. The new species E. estuarinus sp. nov. clusters with E. curdsi, differing only by 1 bp in their SSU rRNA gene sequences, which is likely due to the recent speciation event and the limited resolution of the SSU rRNA gene at species level in this group as the two species are clearly morphologically distinct.
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Affiliation(s)
- Ying Yan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yangbo Fan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; School of Civil and Environment Engineering, Harbin Institute of Technology, Shenzhen 518000, China
| | - Xiaotian Luo
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Hamed A El-Serehy
- Department of Zoology, King Saud University, Riyadh 11451, Saudi Arabia
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise 83725, USA
| | - Xiangrui Chen
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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17
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Chen X, Wang Y, Sheng Y, Warren A, Gao S. GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes. Mol Ecol Resour 2018; 18:700-713. [DOI: 10.1111/1755-0998.12750] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Xiao Chen
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yurui Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
- Laboratory for Marine Biology and Biotechnology; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- College of Marine Life Sciences; Ocean University of China; Qingdao China
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18
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Huang JB, Zhang T, Zhang Q, Li Y, Warren A, Pan H, Yan Y. Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data. ZOOL SCR 2018. [DOI: 10.1111/zsc.12269] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie B. Huang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
| | - Tengteng Zhang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
| | - Qianqian Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation; Yantai Institute of Coastal Zone Research; Chinese Academy of Science; Yantai China
| | - Yuan Li
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; London UK
| | - Hongbo Pan
- College of Oceanography; Hohai University; Nanjing China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
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19
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Wang Y, Chen X, Sheng Y, Liu Y, Gao S. N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena. Nucleic Acids Res 2017; 45:11594-11606. [PMID: 29036602 PMCID: PMC5714169 DOI: 10.1093/nar/gkx883] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/12/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing. We provide evidence that 6mA occurs mostly in the AT motif of the linker DNA regions. More strikingly, these linker DNA regions with 6mA are usually flanked by well-positioned nucleosomes and/or H2A.Z-containing nucleosomes. We also find that 6mA is exclusively associated with RNA polymerase II (Pol II)-transcribed genes, but is not an unambiguous mark for active transcription. These results support that 6mA is an integral part of the chromatin landscape shaped by adenosine triphosphate (ATP)-dependent chromatin remodeling and transcription.
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Affiliation(s)
- Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shan Gao
- 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 266003, China
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20
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Fuse T, Katsumata K, Morohoshi K, Mukai Y, Ichikawa Y, Kurumizaka H, Yanagida A, Urano T, Kato H, Shimizu M. Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. PLoS One 2017; 12:e0186974. [PMID: 29073207 PMCID: PMC5658119 DOI: 10.1371/journal.pone.0186974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
Micrococcal nuclease (MNase) has been widely used for analyses of nucleosome locations in many organisms. However, due to its sequence preference, the interpretations of the positions and occupancies of nucleosomes using MNase have remained controversial. Next-generation sequencing (NGS) has also been utilized for analyses of MNase-digests, but some technical biases are commonly present in the NGS experiments. Here, we established a gel-based method to map nucleosome positions in Saccharomyces cerevisiae, using isolated nuclei as the substrate for the histone H4 S47C-site-directed chemical cleavage in parallel with MNase digestion. The parallel mapping allowed us to compare the chemically and enzymatically cleaved sites by indirect end-labeling and primer extension mapping, and thus we could determine the nucleosome positions and the sizes of the nucleosome-free regions (or nucleosome-depleted regions) more accurately, as compared to nucleosome mapping by MNase alone. The analysis also revealed that the structural features of the nucleosomes flanked by the nucleosome-free region were different from those within regularly arrayed nucleosomes, showing that the structures and dynamics of individual nucleosomes strongly depend on their locations. Moreover, we demonstrated that the parallel mapping results were generally consistent with the previous genome-wide chemical mapping and MNase-Seq results. Thus, the gel-based parallel mapping will be useful for the analysis of a specific locus under various conditions.
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Affiliation(s)
- Tomohiro Fuse
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Koji Katsumata
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Koya Morohoshi
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
| | - Yukio Mukai
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Yuichi Ichikawa
- Graduate School of Advanced Science and Engineering/RISE/IMSB, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering/RISE/IMSB, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Akio Yanagida
- School of Pharmacy, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Shimane, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, Izumo, Shimane, Japan
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan
- * E-mail:
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21
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Wang Y, Wang Y, Sheng Y, Huang J, Chen X, AL-Rasheid KA, Gao S. A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena , Paramecium and Oxytricha. Eur J Protistol 2017; 61:376-387. [DOI: 10.1016/j.ejop.2017.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
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22
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Qu Z, Pan H, Lin X, Li L, Aleidan AMA, Al-Farraj SA, Stoeck T, Hu X. A Contribution to the Morphology and Phylogeny of Chlamydodon, with Three New Species from China (Ciliophora, Cyrtophoria). J Eukaryot Microbiol 2017; 65:236-249. [PMID: 28888076 DOI: 10.1111/jeu.12472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/15/2017] [Accepted: 09/01/2017] [Indexed: 11/27/2022]
Abstract
Three new cyrtophorian ciliates isolated from coastal areas of China were described based on morphological and genetic data. The Chlamydodon mnemosyne-like species Chlamydodon similis sp. n. differs from its congeners mainly by its number of somatic kineties. Chlamydodon oligochaetus sp. n. is distinguished from its congeners mainly by having fewer somatic kineties, and/or an elongated body shape. Chlamydodon crassidens sp. n. is characterized mainly by an inverted triangular body shape, a posteriorly interrupted cross-striated band (5-6 μm wide), and a large cytostome. Moreover, we provided small-subunit (SSU) rDNA sequences of C. similis sp. n. and C. oligochaetus sp. n. Maximum likelihood (ML) and Bayesian inference (BI) consistently placed C. similis sp. n. as a sister to C. paramnemosyne, but showed different branching position of C. oligochaetus sp. n., which may be due to a low taxon sampling in the Chlamydodontidae and/or an insufficient resolution of the marker gene at species level.
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Affiliation(s)
- Zhishuai Qu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Hongbo Pan
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaofeng Lin
- College of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Lifang Li
- Marine College, Shandong University, Weihai, 264209, China
| | | | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Xiaozhong Hu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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23
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Wang Y, Sheng Y, Liu Y, Pan B, Huang J, Warren A, Gao S. N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila. Eur J Protistol 2017; 58:94-102. [DOI: 10.1016/j.ejop.2016.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 01/30/2023]
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24
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Pan X, Shi Z, Wang C, Bourland WA, Chen Y, Song W. Molecular Phylogeny and Taxonomy of a New Freshwater Hymenostomatid from Northeastern China, with the Establishment of a New Genus Anteglaucoma
gen. n. (Protista, Ciliophora, Oligohymenophorea). J Eukaryot Microbiol 2016; 64:564-572. [DOI: 10.1111/jeu.12382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/28/2016] [Accepted: 10/28/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Xuming Pan
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Zihan Shi
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - William A. Bourland
- Department of Biological Sciences; Boise State University; Boise Idaho 83725-1515
| | - Ying Chen
- College of Life Science and Technology; Harbin Normal University; Harbin 150025 China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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