1
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Geng S, Lv X, Xu T. PIF/harbinger transposon-derived protein promotes 7SL expression to enhance pathogen resistance. EMBO Rep 2025; 26:1196-1211. [PMID: 39885293 PMCID: PMC11893794 DOI: 10.1038/s44319-025-00379-8] [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: 03/29/2024] [Revised: 01/14/2025] [Accepted: 01/17/2025] [Indexed: 02/01/2025] Open
Abstract
Transcriptional regulation governs gene expression levels, primarily controlled by "cis-acting DNA elements" and "trans-acting protein factors". However, the conventional view that cis-regulation is solely attributable to DNA elements is challenged in this study. Our research indicates that transposon-derived proteins may retain their original DNA-binding preference and exert cis-regulatory effects on nearby genes on the chromosome, thus denoted as "cis-acting factors". Specifically, we show that the ADF-1L protein, derived from the PIF/harbinger transposon, recruits the histone acetyltransferase KAT2B in a MADF domain-dependent manner, facilitating its own nuclear translocation and binding to and cis-regulating its own and adjacent gene 7SL-23. ADF-1L protein also boosts the host's resistance to pathogens by promoting the expression of immune molecule 7SL RNA. In summary, our findings expand the types of molecules that can exert cis-function in gene regulation and underscore the relevance of transposons-derived sequences in cellular processes.
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Affiliation(s)
- Shang Geng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China.
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2
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Shi Y, Jiang N, Jiang W, Chen J, Wu L, Jiao Y, Zhou Y, Wu L, Huang Y, Li D, Kumar V, Hu B, Huang J. OsHARBI1-1 enhances cadmium tolerance in yeast through YAP1 mediated modulation of cell wall integrity genes and catalase genes. FASEB J 2025; 39:e70346. [PMID: 39902812 DOI: 10.1096/fj.202400111r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/01/2025] [Accepted: 01/15/2025] [Indexed: 02/06/2025]
Abstract
Harbinger transposase-derived 1 proteins (HARBI1s) play important roles in plant growth, development, and response to abiotic stress. OsHARBI1-1 has been identified as a gene encoding HARBI1-1 protein in rice and has been shown to be responsive to Cadmium (Cd) stress. However, the function of OsHARBI1-1 protein under heavy metal stress remains unclear. In this study, the function of a novel rice Cd-responsive gene, OsHARBI1-1, under Cd stress was characterized by heterologous expression in yeast. The heterologous expression OsHARBI1-1 conferred yeast with increased tolerance to Cd. In addition, the yeast cells expressing OsHARBI1-1 exhibited enhanced tolerance to Congo red and exhibited an increase in cell wall thickness under Cd stress, suggesting a potential correlation between increased Cd tolerance and cell wall thickness in the transgenic yeast. When OsHARBI1-1 was expressed in ∆yap1 or ∆yap1∆ycf1 yeast mutants, there was no significant difference in the tolerance of transgenic yeast to Cd and Congo red, as well as in cell wall thickness compared to the control. Meanwhile, the expression of cell wall integrity (CWI) genes and catalase genes in transgenic yeast was up-regulated in a YAP1-dependent manner under Cd or Congo red stress. The above facts supported the inference that OsHARBI1-1 may counteract Cd toxicity by enhancing the expression of YAP1, thereby increasing the thickness of the cell wall and activating the expression of catalase genes.
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Affiliation(s)
- Yang Shi
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Nan Jiang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Wenjun Jiang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Ji Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Lijuan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuan Jiao
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Yingxu Zhou
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Longying Wu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Yanyan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Deqiang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Vinod Kumar
- Algal Research and Bioenergy Laboratory, Department of Food Science and Technology, Graphic Era (Deemed to be University), Dehradun, India
| | - Binhua Hu
- Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jin Huang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
- Key Laboratory of Monitoring for Heavy Metal Pollutants, Ministry of Ecology and Environment, Changsha, China
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3
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Tamagawa K, Campbell RE, Terai T. High-Throughput Discovery of Substrate Peptide Sequences for E3 Ubiquitin Ligases Using a cDNA Display Method. Chembiochem 2024; 25:e202400617. [PMID: 39512024 DOI: 10.1002/cbic.202400617] [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: 07/24/2024] [Revised: 10/21/2024] [Accepted: 11/07/2024] [Indexed: 11/15/2024]
Abstract
Cells utilize ubiquitin as a posttranslational protein modifier to convey various signals such as proteasomal degradation. The dysfunction of ubiquitylation or following proteasomal degradation can give rise to the accumulation and aggregation of improperly ubiquitylated proteins, which is known to be a general causation of many neurodegenerative diseases. Thus, the characterization of substrate peptide sequences of E3 ligases is crucial in biological and pharmaceutical sciences. In this study, we developed a novel high-throughput screening system for substrate peptide sequences of E3 ligases using a cDNA display method, which enables covalent conjugation between peptide sequences and their corresponding cDNA sequences. First, we focused on the MDM2 E3 ligase and its known peptide substrate as a model to establish the screening method, and confirmed that cDNA display method was compatible with in vitro ubiquitylation. Then, we demonstrated identification of MDM2 substrate sequences from random libraries to identify a novel motif (VKFTGGQLA). Bioinformatics analysis of the hit sequences was performed to gain insight about endogenous substrate proteins.
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Affiliation(s)
- Kenwa Tamagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Robert E Campbell
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Terai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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4
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Zhou Z, Shao G, Shen Y, He F, Tu X, Ji J, Ao J, Chen X. Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass ( Lateolabrax maculatus) Using Whole-Genome Resequencing. Animals (Basel) 2024; 14:2995. [PMID: 39457925 PMCID: PMC11503831 DOI: 10.3390/ani14202995] [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: 08/23/2024] [Revised: 10/09/2024] [Accepted: 10/15/2024] [Indexed: 10/28/2024] Open
Abstract
Spotted sea bass (Lateolabrax maculatus) is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of L. maculatus and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in L. maculatus. Two groups of L. maculatus, consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained (PVE) reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of L. maculatus. Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of L. maculatus through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits.
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Affiliation(s)
- Zhaolong Zhou
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Guangming Shao
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Yibo Shen
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Fengjiao He
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Xiaomei Tu
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Jiawen Ji
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Jingqun Ao
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
| | - Xinhua Chen
- Fuzhou Institute of Oceanography, State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (G.S.); (Y.S.); (F.H.); (X.T.); (J.J.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
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5
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Zhang T, Tan S, Tang N, Li Y, Zhang C, Sun J, Guo Y, Gao H, Cai Y, Sun W, Wang C, Fu L, Ma H, Wu Y, Hu X, Zhang X, Gee P, Yan W, Zhao Y, Chen Q, Guo B, Wang H, Zhang YE. Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell 2024; 187:3741-3760.e30. [PMID: 38843831 DOI: 10.1016/j.cell.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 07/14/2024]
Abstract
Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.
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Affiliation(s)
- Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Tang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yuanqing Li
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jing Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Gao
- Rengene Biotechnology Co., Ltd., Beijing 100036, China
| | - Yujia Cai
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxin Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liangzheng Fu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yachao Wu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Peter Gee
- MaxCyte Inc., Rockville, MD 20850, USA
| | - Weihua Yan
- Cold Spring Biotech Corp., Beijing 100031, China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Baocheng Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Huang HY, Zhang S, Choucha FA, Verdenaud M, Tan FQ, Pichot C, Parsa HS, Slavkovic F, Chen Q, Troadec C, Marcel F, Dogimont C, Quadrana L, Boualem A, Bendahmane A. Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits. Nat Commun 2024; 15:4877. [PMID: 38849342 PMCID: PMC11161486 DOI: 10.1038/s41467-024-49250-9] [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: 12/12/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
In flowering plants, the predominant sexual morph is hermaphroditism, and the emergence of unisexuality is poorly understood. Using Cucumis melo (melon) as a model system, we explore the mechanisms driving sexual forms. We identify a spontaneous mutant exhibiting a transition from bisexual to unisexual male flower, and identify the causal mutation as a Harbinger transposon impairing the expression of Ethylene Insensitive 2 (CmEIN2) gene. Genetics and transcriptomic analysis reveal a dual role of CmEIN2 in both sex determination and fruit shape formation. Upon expression of CmACS11, EIN2 is recruited to repress the expression of the carpel inhibitor, CmWIP1. Subsequently, EIN2 is recruited to mediate stamina inhibition. Following the sex determination phase, EIN2 promotes fruit shape elongation. Genome-wide analysis reveals that Harbinger transposon mobilization is triggered by environmental cues, and integrates preferentially in active chromatin, particularly within promoter regions. Characterization of a large collection of melon germplasm points to active transpositions in the wild, compared to cultivated accessions. Our study underscores the association between chromatin dynamics and the temporal aspects of mobile genetic element insertions, providing valuable insights into plant adaptation and crop genome evolution.
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Affiliation(s)
- Hsin-Ya Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Siqi Zhang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Fadi Abou Choucha
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Marion Verdenaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Feng-Quan Tan
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Clement Pichot
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Hadi Shirazi Parsa
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Filip Slavkovic
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Qinghe Chen
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Fabien Marcel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Catherine Dogimont
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143, Montfavet, France
| | - Leandro Quadrana
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190, Gif-sur-Yvette, France.
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7
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Jiang N, Shi Y, Li M, Du Z, Chen J, Jiang W, Huang Y, Zhong M, Yang J, Hu B, Huang J. Expression of OsHARBI1-1 enhances the tolerance of Arabidopsis thaliana to cadmium. BMC PLANT BIOLOGY 2023; 23:556. [PMID: 37950159 PMCID: PMC10638780 DOI: 10.1186/s12870-023-04540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND As one of the major food crops in the world, rice is vulnerable to cadmium (Cd) pollution. Understanding of the molecular mechanisms of Cd uptake, transport and detoxification in rice is essential for the breeding of low-Cd rice. However, the molecular mechanisms underlying the response of rice to Cd stress remains to be further clarified. RESULTS In this study, a novel Cd-responsive gene OsHARBI1-1 was identified in the rice genome and its expression pattern and function were characterized. Bioinformatics analysis showed that the promoter region of OsHARBI1-1 had multiple cis-acting elements in response to phytohormones and stress, and the expression of OsHARBI1-1 was induced by phytohormones. OsHARBI1-1 protein was targeted to the nucleus. qRT-PCR analysis results showed that the expression of OsHARBI1-1 in the roots was repressed while the expression in the shoots was increased under Cd stress. Heterologous expression of OsHARBI1-1 in yeast conferred tolerance to Cd and reduced Cd content in the cells. Meanwhile, the expression of OsHARBI1-1 in Arabidopsis thaliana (A. thaliana) enhanced the tolerance of A. thaliana to Cd stress. In addition, compared with the wild type plants, the POD activity of transgenic plants was increased, while the SOD and CAT activities were decreased. Interestingly, the accumulation of Cd in the roots of A. thaliana expressing OsHARBI1-1 was significantly increased, whereas the Cd accumulation in the shoots was slightly decreased. Compared to the WT plants, the expression of genes related to Cd absorption and chelation was upregulated in transgenic A. thaliana under Cd stress, while the expression of genes responsible for the translocation of Cd from the roots to the shoots was downregulated. Moreover, the expression of phytohormone-related genes was significantly influenced by the expression of OsHARBI1-1 with and without Cd treatment. CONCLUSIONS Findings of this study suggest that OsHARBI1-1 might play a role in the response of plants to Cd response by affecting antioxidant enzyme activities, Cd chelation, absorption and transport, and phytohormone homeostasis and signaling.
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Affiliation(s)
- Nan Jiang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Yang Shi
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Mingyu Li
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Zhiye Du
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Ji Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenjun Jiang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Yanyan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhong
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Ju Yang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China
| | - Binhua Hu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jin Huang
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, China.
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8
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Redd PS, Payero L, Gilbert DM, Page CA, King R, McAssey EV, Bodie D, Diaz S, Hancock CN. Transposase expression, element abundance, element size, and DNA repair determine the mobility and heritability of PIF/ Pong/ Harbinger transposable elements. Front Cell Dev Biol 2023; 11:1184046. [PMID: 37363729 PMCID: PMC10288884 DOI: 10.3389/fcell.2023.1184046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Class II DNA transposable elements account for significant portions of eukaryotic genomes and contribute to genome evolution through their mobilization. To escape inactivating mutations and persist in the host genome over evolutionary time, these elements must be mobilized enough to result in additional copies. These elements utilize a "cut and paste" transposition mechanism that does not intrinsically include replication. However, elements such as the rice derived mPing element have been observed to increase in copy number over time. Methods: We used yeast transposition assays to test several parameters that could affect the excision and insertion of mPing and its related elements. This included development of novel strategies for measuring element insertion and sequencing insertion sites. Results: Increased transposase protein expression increased the mobilization frequency of a small (430 bp) element, while overexpression inhibition was observed for a larger (7,126 bp) element. Smaller element size increased both the frequency of excision and insertion of these elements. The effect of yeast ploidy on element excision, insertion, and copy number provided evidence that homology dependent repair allows for replicative transposition. These elements were found to preferentially insert into yeast rDNA repeat sequences. Discussion: Identifying the parameters that influence transposition of these elements will facilitate their use for gene discovery and genome editing. These insights in to the behavior of these elements also provide important clues into how class II transposable elements have shaped eukaryotic genomes.
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Affiliation(s)
- Priscilla S. Redd
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Lisette Payero
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - David M. Gilbert
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Clinton A. Page
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Reese King
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Edward V. McAssey
- Department of Crop and Soil Science, Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, United States
| | - Dalton Bodie
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Stephanie Diaz
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - C. Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
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9
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Redd PS, Diaz S, Weidner D, Benjamin J, Hancock CN. Mobility of mPing and its associated elements is regulated by both internal and terminal sequences. Mob DNA 2023; 14:1. [PMID: 36774502 PMCID: PMC9921582 DOI: 10.1186/s13100-023-00289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/04/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND DNA transposable elements are mobilized by a "cut and paste" mechanism catalyzed by the binding of one or more transposase proteins to terminal inverted repeats (TIRs) to form a transpositional complex. Study of the rice genome indicates that the mPing element has experienced a recent burst in transposition compared to the closely related Ping and Pong elements. A previously developed yeast transposition assay allowed us to probe the role of both internal and terminal sequences in the mobilization of these elements. RESULTS We observed that mPing and a synthetic mPong element have significantly higher transposition efficiency than the related autonomous Ping and Pong elements. Systematic mutation of the internal sequences of both mPing and mPong identified multiple regions that promote or inhibit transposition. Simultaneous alteration of single bases on both mPing TIRs resulted in a significant reduction in transposition frequency, indicating that each base plays a role in efficient transposase binding. Testing chimeric mPing and mPong elements verified the important role of both the TIRs and internal regulatory regions. Previous experiments showed that the G at position 16, adjacent to the 5' TIR, allows mPing to have higher mobility. Alteration of the 16th and 17th base from mPing's 3' end or replacement of the 3' end with Pong 3' sequences significantly increased transposition frequency. CONCLUSIONS As the transposase proteins were consistent throughout this study, we conclude that the observed transposition differences are due to the element sequences. The presence of sub-optimal internal regions and TIR bases supports a model in which transposable elements self-limit their activity to prevent host damage and detection by host regulatory mechanisms. Knowing the role of the TIRs, adjacent sub-TIRs, and internal regulatory sequences allows for the creation of hyperactive elements.
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Affiliation(s)
- Priscilla S. Redd
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
| | - Stephanie Diaz
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA ,grid.66859.340000 0004 0546 1623Present address: Bayer Pharmaceuticals, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - David Weidner
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
| | - Jazmine Benjamin
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA ,grid.265892.20000000106344187Present address: Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - C. Nathan Hancock
- grid.267160.40000 0000 9205 7135Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801 USA
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10
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Markova DN, Ruma FB, Casola C, Mirsalehi A, Betrán E. Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects. Mob DNA 2022; 13:28. [PMID: 36451208 PMCID: PMC9710019 DOI: 10.1186/s13100-022-00282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are selfish DNA sequences capable of moving and amplifying at the expense of host cells. Despite this, an increasing number of studies have revealed that TE proteins are important contributors to the emergence of novel host proteins through molecular domestication. We previously described seven transposase-derived domesticated genes from the PIF/Harbinger DNA family of TEs in Drosophila and a co-domestication. All PIF TEs known in plants and animals distinguish themselves from other DNA transposons by the presence of two genes. We hypothesize that there should often be co-domestications of the two genes from the same TE because the transposase (gene 1) has been described to be translocated to the nucleus by the MADF protein (gene 2). To provide support for this model of new gene origination, we investigated available insect species genomes for additional evidence of PIF TE domestication events and explored the co-domestication of the MADF protein from the same TE insertion. RESULTS After the extensive insect species genomes exploration of hits to PIF transposases and analyses of their context and evolution, we present evidence of at least six independent PIF transposable elements proteins domestication events in insects: two co-domestications of both transposase and MADF proteins in Anopheles (Diptera), one transposase-only domestication event and one co-domestication in butterflies and moths (Lepidoptera), and two transposases-only domestication events in cockroaches (Blattodea). The predicted nuclear localization signals for many of those proteins and dicistronic transcription in some instances support the functional associations of co-domesticated transposase and MADF proteins. CONCLUSIONS Our results add to a co-domestication that we previously described in fruit fly genomes and support that new gene origination through domestication of a PIF transposase is frequently accompanied by the co-domestication of a cognate MADF protein in insects, potentially for regulatory functions. We propose a detailed model that predicts that PIF TE protein co-domestication should often occur from the same PIF TE insertion.
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Affiliation(s)
- Dragomira N. Markova
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Fatema B. Ruma
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Claudio Casola
- grid.264756.40000 0004 4687 2082Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX USA
| | - Ayda Mirsalehi
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
| | - Esther Betrán
- grid.267315.40000 0001 2181 9515Department of Biology, University of Texas at Arlington, Arlington, TX USA
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11
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Etchegaray E, Baas D, Naville M, Haftek-Terreau Z, Volff JN. The neurodevelopmental gene MSANTD2 belongs to a gene family formed by recurrent molecular domestication of Harbinger transposons at the base of vertebrates. Mol Biol Evol 2022; 39:msac173. [PMID: 35980103 PMCID: PMC9392472 DOI: 10.1093/molbev/msac173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
The formation of new genes is a major source of organism evolutionary innovation. Beyond their mutational effects, transposable elements can be co-opted by host genomes to form different types of sequences including novel genes, through a mechanism named molecular domestication.We report the formation of four genes through molecular domestication of Harbinger transposons, three in a common ancestor of jawed vertebrates about 500 million years ago and one in sarcopterygians approx. 430 million years ago. Additionally, one processed pseudogene arose approx. 60 million years ago in simians. In zebrafish, Harbinger-derived genes are expressed during early development but also in adult tissues, and predominantly co-expressed in male brain. In human, expression was detected in multiple organs, with major expression in the brain particularly during fetal development. We used CRISPR/Cas9 with direct gene knock-out in the F0 generation and the morpholino antisense oligonucleotide knock-down technique to study in zebrafish the function of one of these genes called MSANTD2, which has been suggested to be associated to neuro-developmental diseases such as autism spectrum disorders and schizophrenia in human. MSANTD2 inactivation led to developmental delays including tail and nervous system malformation at one day post fertilization. Affected embryos showed dead cell accumulation, major anatomical defects characterized by impaired brain ventricle formation and alterations in expression of some characteristic genes involved in vertebrate nervous system development. Hence, the characterization of MSANTD2 and other Harbinger-derived genes might contribute to a better understanding of the genetic innovations having driven the early evolution of the vertebrate nervous system.
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Affiliation(s)
- Ema Etchegaray
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Dominique Baas
- Unité MeLiS, UCBL-CNRS UMR 5284, INSERM U1314, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Jean Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
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12
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Etchegaray E, Dechaud C, Barbier J, Naville M, Volff JN. Diversity of Harbinger-like Transposons in Teleost Fish Genomes. Animals (Basel) 2022; 12:ani12111429. [PMID: 35681893 PMCID: PMC9179366 DOI: 10.3390/ani12111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The study of transposable elements, which are repeated DNA sequences that can insert into new locations in genomes, is of particular interest to genome evolution, as they are sources of mutations but also of new regulatory and coding sequences. Teleost fish are a species-rich clade presenting a high diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger-like DNA transposons, which are widespread from plants to vertebrates but absent from mammalian genomes. These elements code for both a transposase and a Myb-like protein. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish. While Harbinger transposons might have been present in a common ancestor of all the fish species studied, ISL2EU elements were possibly gained by horizontal transfer at the base of teleost fish. Transposase and Myb-like protein phylogenies of Harbinger transposons indicated unique origins of the association between both genes and suggests recombination was rare between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish. Abstract Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.
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13
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Plooster M, Rossi G, Farrell MS, McAfee JC, Bell JL, Ye M, Diering GH, Won H, Gupton SL, Brennwald P. Schizophrenia-Linked Protein tSNARE1 Regulates Endosomal Trafficking in Cortical Neurons. J Neurosci 2021; 41:9466-9481. [PMID: 34642214 PMCID: PMC8580139 DOI: 10.1523/jneurosci.0556-21.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
TSNARE1, which encodes the protein tSNARE1, is a high-confidence gene candidate for schizophrenia risk, but nothing is known about its cellular or physiological function. We identified the major gene products of TSNARE1 and their cytoplasmic localization and function in endosomal trafficking in cortical neurons. We validated three primary isoforms of TSNARE1 expressed in human brain, all of which encode a syntaxin-like Qa SNARE domain. RNA-sequencing data from adult and fetal human brain suggested that the majority of tSNARE1 lacks a transmembrane domain that is thought to be necessary for membrane fusion. Biochemical data demonstrate that tSNARE1 can compete with Stx12 for incorporation into an endosomal SNARE complex, supporting its possible role as an inhibitory SNARE. Live-cell imaging in cortical neurons from mice of both sexes demonstrated that brain tSNARE1 isoforms localized to the endosomal network. The most abundant brain isoform, tSNARE1c, localized most frequently to Rab7+ late endosomes, and endogenous tSNARE1 displayed a similar localization in human neural progenitor cells and neuroblastoma cells. In mature rat neurons from both sexes, tSNARE1 localized to the dendritic shaft and dendritic spines, supporting a role for tSNARE1 at the postsynapse. Expression of either tSNARE1b or tSNARE1c, which differ only in their inclusion or exclusion of an Myb-like domain, delayed the trafficking of the dendritic endosomal cargo Nsg1 into late endosomal and lysosomal compartments. These data suggest that tSNARE1 regulates endosomal trafficking in cortical neurons, likely by negatively regulating early endosomal to late endosomal trafficking.SIGNIFICANCE STATEMENT Schizophrenia is a severe and polygenic neuropsychiatric disorder. Understanding the functions of high-confidence candidate genes is critical toward understanding how their dysfunction contributes to schizophrenia pathogenesis. TSNARE1 is one of the high-confidence candidate genes for schizophrenia risk, yet nothing was known about its cellular or physiological function. Here we describe the major isoforms of TSNARE1 and their cytoplasmic localization and function in the endosomal network in cortical neurons. Our results are consistent with the hypothesis that the majority of brain tSNARE1 acts as a negative regulator to endolysosomal trafficking.
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Affiliation(s)
- Melissa Plooster
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Guendalina Rossi
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Martilias S Farrell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jessica C McAfee
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jessica L Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Michael Ye
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Graham H Diering
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Hyejung Won
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Stephanie L Gupton
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Patrick Brennwald
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
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14
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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15
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Luo H, Zhang Y, Deng Y, Li L, Sheng Z, Yu Y, Lin Y, Chen X, Feng P. Nxhl Controls Angiogenesis by Targeting VE-PTP Through Interaction With Nucleolin. Front Cell Dev Biol 2021; 9:728821. [PMID: 34733844 PMCID: PMC8558974 DOI: 10.3389/fcell.2021.728821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Precise regulation of angiogenesis is required for organ development, wound repair, and tumor progression. Here, we identified a novel gene, nxhl (New XingHuo light), that is conserved in vertebrates and that plays a crucial role in vascular integrity and angiogenesis. Bioinformatic analysis uncovered its essential roles in development based on co-expression with several key developmental genes. Knockdown of nxhl in zebrafish causes global and pericardial edema, loss of blood circulation, and vascular defects characterized by both reduced vascularization in intersegmental vessels and decreased sprouting in the caudal vein plexus. The nxhl gene also affects human endothelial cell behavior in vitro. We found that nxhl functions in part by targeting VE-PTP through interaction with NCL (nucleolin). Loss of ptprb (a VE-PTP ortholo) in zebrafish resulted in defects similar to nxhl knockdown. Moreover, nxhl deficiency attenuates tumor invasion and proteins (including VE-PTP and NCL) associated with angiogenesis and EMT. These findings illustrate that nxhl can regulate angiogenesis via a novel nxhl-NCL-VE-PTP axis, providing a new therapeutic target for modulating vascular formation and function, especially for cancer treatment.
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Affiliation(s)
- Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China.,Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yanfei Deng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lequn Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zhaoan Sheng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yanling Yu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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16
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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17
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Liu X, Xie H, Fu Z, Yao Q, Han T, Zhan D, Lin Z, Zhu H. MAD1L1 and TSNARE gene polymorphisms are associated with schizophrenia susceptibility in the Han Chinese population. BMC Med Genomics 2021; 14:218. [PMID: 34481484 PMCID: PMC8418747 DOI: 10.1186/s12920-021-01070-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/23/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Schizophrenia (SCZ) is a severe mental illness with high heritability. This study aimed to explore the correlation between MAD1L1, TSNARE polymorphisms and SCZ susceptibility. METHODS A total of 493 SCZ patients and 493 healthy controls were included. The genotypes of MAD1L1 and TSNARE polymorphisms were identified by Agena MassARRAY platform. Odds ratio (OR) and 95% confidence intervals (CIs) were tested via logistic regression analysis in multiple genetic models and different subgroups. RESULTS We observed that AG genotype of rs1107592, AG genotype of rs4976976, and CA genotype of rs67756423 decreased the susceptibility to SCZ (p < 0.05). Age stratification analysis showed that the TC genotype of rs12666575, AG genotype of rs1107592, and AG genotype of rs4976976 decreased the risk of SCZ individuals older than 36 years (p < 0.05). In addition, the AG and AA genotype of rs4976976, the CA genotype of rs67756423 were associated with a lower risk of SCZ in males (p < 0.05). In females, the TT genotype of rs12666575 in recessive model, the AG and AA-AG genotype of rs1107592 in heterozygote and dominant model, could reduce the susceptibility to SCZ (p < 0.05). However, no significant association was found after Bonferroni correction. CONCLUSIONS Our results suggest that MAD1L1 and TSNARE genetic polymorphisms exert a protective role in the risk of SCZ. These findings provide evidence that MAD1L1 and TSNARE may serve as potential biomarkers of SCZ. However, a replication experiment in a cohort with large sample size are required to confirm our findings. Trial registration Not applicable.
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Affiliation(s)
- Xianglai Liu
- Institute of Mental Health, Hainan Provincial Anning Hospital, No 10, Nanhai Avenue East, Haikou, 571100, Hainan, China.
| | - Hailing Xie
- First Department of Psychiatry, Hainan Provincial Anning Hospital, Haikou, 571100, Hainan, China
| | - Zejuan Fu
- Department of Nursing, Hainan Provincial Anning Hospital, Haikou, 571100, Hainan, China
| | - Qiankun Yao
- Department of Prevention Section, Hainan Provincial Anning Hospital, Haikou, 571100, Hainan, China
| | - Tianming Han
- Institute of Mental Health, Hainan Provincial Anning Hospital, No 10, Nanhai Avenue East, Haikou, 571100, Hainan, China
| | - Dafei Zhan
- Institute of Mental Health, Hainan Provincial Anning Hospital, No 10, Nanhai Avenue East, Haikou, 571100, Hainan, China
| | - Zhan Lin
- Institute of Mental Health, Hainan Provincial Anning Hospital, No 10, Nanhai Avenue East, Haikou, 571100, Hainan, China
| | - Hong Zhu
- Institute of Mental Health, Hainan Provincial Anning Hospital, No 10, Nanhai Avenue East, Haikou, 571100, Hainan, China
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18
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Galbraith JD, Ludington AJ, Sanders KL, Suh A, Adelson DL. Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda). Biol Lett 2021; 17:20210342. [PMID: 34464541 PMCID: PMC8437027 DOI: 10.1098/rsbl.2021.0342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are self-replicating genetic sequences and are often described as important 'drivers of evolution'. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions potentially lead to neutral or harmful outcomes, therefore host genomes have evolved machinery to suppress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonize new genomes, and since new hosts may not be able to regulate subsequent replication, these TEs may proliferate rapidly. Here, we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids approximately 15-25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8-12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.
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Affiliation(s)
- James D. Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | | | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala SE-752 36, Sweden
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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19
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Zhou X, He J, Velanis CN, Zhu Y, He Y, Tang K, Zhu M, Graser L, de Leau E, Wang X, Zhang L, Andy Tao W, Goodrich J, Zhu JK, Zhang CJ. A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1462-1474. [PMID: 33960113 DOI: 10.1111/jipb.13108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants.
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Affiliation(s)
- Xishi Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Junna He
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Christos N Velanis
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yuhan He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Mingku Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lisa Graser
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
- University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10,, Mannheim, 68163, Germany
| | - Erica de Leau
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Lingrui Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette,, IN 47907, USA
| | - Justin Goodrich
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Cui-Jun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
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20
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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21
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Verissimo KM, Perez LN, Dragalzew AC, Senevirathne G, Darnet S, Barroso Mendes WR, Ariel Dos Santos Neves C, Monteiro Dos Santos E, Nazare de Sousa Moraes C, Elewa A, Shubin N, Fröbisch NB, de Freitas Sousa J, Schneider I. Salamander-like tail regeneration in the West African lungfish. Proc Biol Sci 2020; 287:20192939. [PMID: 32933441 DOI: 10.1098/rspb.2019.2939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Salamanders, frog tadpoles and diverse lizards have the remarkable ability to regenerate tails. Palaeontological data suggest that this capacity is plesiomorphic, yet when the developmental and genetic architecture of tail regeneration arose is poorly understood. Here, we show morphological and molecular hallmarks of tetrapod tail regeneration in the West African lungfish Protopterus annectens, a living representative of the sister group of tetrapods. As in salamanders, lungfish tail regeneration occurs via the formation of a proliferative blastema and restores original structures, including muscle, skeleton and spinal cord. In contrast with lizards and similar to salamanders and frogs, lungfish regenerate spinal cord neurons and reconstitute dorsoventral patterning of the tail. Similar to salamander and frog tadpoles, Shh is required for lungfish tail regeneration. Through RNA-seq analysis of uninjured and regenerating tail blastema, we show that the genetic programme deployed during lungfish tail regeneration maintains extensive overlap with that of tetrapods, with the upregulation of genes and signalling pathways previously implicated in amphibian and lizard tail regeneration. Furthermore, the lungfish tail blastema showed marked upregulation of genes encoding post-transcriptional RNA processing components and transposon-derived genes. Our results show that the developmental processes and genetic programme of tetrapod tail regeneration were present at least near the base of the sarcopterygian clade and establish the lungfish as a valuable research system for regenerative biology.
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Affiliation(s)
- Kellen Matos Verissimo
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900, Belém, Brazil
| | - Louise Neiva Perez
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900, Belém, Brazil.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Aline Cutrim Dragalzew
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900, Belém, Brazil
| | - Gayani Senevirathne
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Sylvain Darnet
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900, Belém, Brazil
| | | | | | | | | | - Ahmed Elewa
- Department of Cell and Molecular Biology, Karolinska Institute, S-171 77, Stockholm, Sweden
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Nadia Belinda Fröbisch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | | | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-900, Belém, Brazil.,Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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22
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Gao B, Wang Y, Diaby M, Zong W, Shen D, Wang S, Chen C, Wang X, Song C. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. Mob DNA 2020; 11:25. [PMID: 32742312 PMCID: PMC7386202 DOI: 10.1186/s13100-020-00220-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood. RESULTS Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains. CONCLUSIONS This is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.
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Affiliation(s)
- Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Mohamed Diaby
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wencheng Zong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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23
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Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J. The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2). PLoS Genet 2020; 16:e1008681. [PMID: 32463832 PMCID: PMC7282668 DOI: 10.1371/journal.pgen.1008681] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/09/2020] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through “domestication”–the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes. A large part of the genomes of plants and animals consists of transposable elements (TE), which are usually considered as selfish or parasitic as they encode proteins (transposases) which promote TE proliferation but not functions useful for their hosts. As a result, hosts have evolved ways of reducing TE proliferation, usually by modifying the DNA or chromatin of TE so that their transposases are no longer produced. Once the TE are inactivated they can no longer proliferate and over time they accumulate mutations and can evolve new functions, often beneficial for their hosts. This process is known as domestication and is increasingly recognised as a potent source of evolutionary novelty. For example, the CRISPR/Cas system that has provided the basis for a revolution in genetic engineering (“genome editing”) has evolved via domestication of transposons in bacteria. We have identified the ALP proteins, two domesticated transposases which function as components of an enzyme complex (PRC2) involved in modifying chromatin and regulating host gene activity in plants. Here we show how ALPs contact PRC2 and direct formation of a novel complex that lacks several of the usual components. The ALPs and related proteins will provide valuable tools for manipulating plant chromatin.
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Affiliation(s)
- Christos N. Velanis
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Pumi Perera
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Erica de Leau
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Shih Chieh Liang
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Ben Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Alexander Förderer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Harry Thornton
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Pedro Arede
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Jiawen Chen
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Kimberly M. Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Serin Gümüs
- Department of Biotechnology, Mannheim University of Applied Science, Mannheim, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
| | - Clinton A. Page
- Department of Biology & Geology, University of South Carolina Aiken, Aiken, South Carolina, United States of America
| | - C. Nathan Hancock
- Department of Biology & Geology, University of South Carolina Aiken, Aiken, South Carolina, United States of America
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Franziska Turck
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Justin Goodrich
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
- * E-mail:
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24
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Kojima KK. Structural and sequence diversity of eukaryotic transposable elements. Genes Genet Syst 2019; 94:233-252. [DOI: 10.1266/ggs.18-00024] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kenji K. Kojima
- Genetic Information Research Institute
- Department of Life Sciences, National Cheng Kung University
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25
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Elewa A, Wang H, Talavera-López C, Joven A, Brito G, Kumar A, Hameed LS, Penrad-Mobayed M, Yao Z, Zamani N, Abbas Y, Abdullayev I, Sandberg R, Grabherr M, Andersson B, Simon A. Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration. Nat Commun 2017; 8:2286. [PMID: 29273779 PMCID: PMC5741667 DOI: 10.1038/s41467-017-01964-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/26/2017] [Indexed: 11/09/2022] Open
Abstract
Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeleswaltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates. The Iberian ribbed newt Pleurodeles waltl has a wide spectrum of regeneration abilities. Here, Elewa et al. sequence its ~20 Gb genome and transcriptome to investigate the molecular features underlying its regenerative capacities.
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Affiliation(s)
- Ahmed Elewa
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.
| | - Heng Wang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.,The Francis Crick Institute, NW1 1AT, London, UK
| | - Alberto Joven
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - Gonçalo Brito
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - Anoop Kumar
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - L Shahul Hameed
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - May Penrad-Mobayed
- Institut Jacques Monod, CNRS & University Paris-Diderot, Paris, 75205, France
| | - Zeyu Yao
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - Neda Zamani
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Yamen Abbas
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Ilgar Abdullayev
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.,Ludwig Institute for Cancer Research, Stockholm, SE-171 65, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.,Ludwig Institute for Cancer Research, Stockholm, SE-171 65, Sweden
| | - Manfred Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, SE-171 65, Sweden.
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Kawakami K, Largaespada DA, Ivics Z. Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 2017; 33:784-801. [PMID: 28888423 DOI: 10.1016/j.tig.2017.07.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats.
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Affiliation(s)
- Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan; These authors contributed equally to this work
| | - David A Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA; These authors contributed equally to this work
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany; These authors contributed equally to this work..
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Duan CG, Wang X, Xie S, Pan L, Miki D, Tang K, Hsu CC, Lei M, Zhong Y, Hou YJ, Wang Z, Zhang Z, Mangrauthia SK, Xu H, Zhang H, Dilkes B, Tao WA, Zhu JK. A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell Res 2016; 27:226-240. [PMID: 27934869 PMCID: PMC5339849 DOI: 10.1038/cr.2016.147] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 12/23/2022] Open
Abstract
Transposons are generally kept silent by epigenetic mechanisms including DNA methylation. Here, we identified a pair of Harbinger transposon-derived proteins (HDPs), HDP1 and HDP2, as anti-silencing factors in Arabidopsis. hdp1 and hdp2 mutants displayed an enhanced silencing of transgenes and some transposons. Phylogenetic analyses revealed that HDP1 and HDP2 were co-domesticated from the Harbinger transposon-encoded transposase and DNA-binding protein, respectively. HDP1 interacts with HDP2 in the nucleus, analogous to their transposon counterparts. Moreover, HDP1 and HDP2 are associated with IDM1, IDM2, IDM3 and MBD7 that constitute a histone acetyltransferase complex functioning in DNA demethylation. HDP2 and the methyl-DNA-binding protein MBD7 share a large set of common genomic binding sites, indicating that they jointly determine the target specificity of the histone acetyltransferase complex. Thus, our data revealed that HDP1 and HDP2 constitute a functional module that has been recruited to a histone acetyltransferase complex to prevent DNA hypermethylation and epigenetic silencing.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Shaojun Xie
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Li Pan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Yingli Zhong
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Yueh-Ju Hou
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Zhijuan Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,The State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050022, China
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Satendra K Mangrauthia
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,Biotechnology Section, Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Huawei Xu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,College of Agriculture, Henan University of Science and Technology, Luoyang, Henan 471026, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
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Ricci WA, Zhang X. Public Service by a Selfish Gene: A Domesticated Transposase Antagonizes Polycomb Function. PLoS Genet 2016; 12:e1006014. [PMID: 27253527 PMCID: PMC4890758 DOI: 10.1371/journal.pgen.1006014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- William A. Ricci
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J. Kicking against the PRCs - A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet 2015; 11:e1005660. [PMID: 26642436 PMCID: PMC4671723 DOI: 10.1371/journal.pgen.1005660] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity. Transposons are parasitic genetic elements that proliferate within their hosts’ genomes. Because rampant transposition is usually deleterious, hosts have evolved ways to inhibit the activity of transposons. In plants, this genome defence is provided by the Polycomb group (PcG) proteins and/or the DNA methylation machinery, which repress the transcription of transposase genes. We identified the Arabidopsis ALP1 gene through its role in opposing gene silencing mediated by PcG genes. ALP1 is an ancient gene in land plants and has evolved from a domesticated transposase. Unexpectedly, we find that the ALP1 protein is present in a conserved complex of PcG proteins that inhibit transcription by methylating the histone proteins that package DNA. ALP1 likely inhibits the activity of this PcG complex by blocking its interaction with accessory proteins that stimulate its activity. We suggest that the inhibition of the PcG by a transposase may originally have evolved as a means for transposons to evade surveillance by their hosts, and that subsequently hosts may have exploited this as a means to regulate PcG activity. Our work illustrates how transposons can be friend or fiend, and raises the question of whether other transposases will also be found to inhibit their host’s regulatory machinery.
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Affiliation(s)
- Shih Chieh Liang
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Ben Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Pumi Perera
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Santiago Mora-García
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Erica de Leau
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Thornton
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Flavia Lima de Alves
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Juri Rapsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Suxin Yang
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | - Franziska Turck
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
- * E-mail: (FT); (JG)
| | - Justin Goodrich
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (FT); (JG)
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Koonin EV, Krupovic M. Evolution of adaptive immunity from transposable elements combined with innate immune systems. Nat Rev Genet 2014; 16:184-92. [PMID: 25488578 DOI: 10.1038/nrg3859] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Adaptive immune systems in prokaryotes and animals give rise to long-term memory through modification of specific genomic loci, such as by insertion of foreign (viral or plasmid) DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci in prokaryotes and by V(D)J recombination of immunoglobulin genes in vertebrates. Strikingly, recombinases derived from unrelated mobile genetic elements have essential roles in both prokaryotic and vertebrate adaptive immune systems. Mobile elements, which are ubiquitous in cellular life forms, provide the only known, naturally evolved tools for genome engineering that are successfully adopted by both innate immune systems and genome-editing technologies. In this Opinion article, we present a general scenario for the origin of adaptive immunity from mobile elements and innate immune systems.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Docteur Roux, 75015 Paris, France
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31
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Han MJ, Xu HE, Zhang HH, Feschotte C, Zhang Z. Spy: a new group of eukaryotic DNA transposons without target site duplications. Genome Biol Evol 2014; 6:1748-57. [PMID: 24966181 PMCID: PMC4122938 DOI: 10.1093/gbe/evu140] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5'-AAA and TTT-3' host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties.
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Affiliation(s)
- Min-Jin Han
- School of Life Sciences, Chongqing University, China
| | - Hong-En Xu
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen, Freising, Germany
| | - Hua-Hao Zhang
- School of Life Sciences, Chongqing University, ChinaCollege of Pharmacy and Life Science, Jiujiang University, China
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine
| | - Ze Zhang
- School of Life Sciences, Chongqing University, China
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32
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Overexpression of nuclear apoptosis-inducing factor 1 altered the proteomic profile of human gastric cancer cell MKN45 and induced cell cycle arrest at G1/S phase. PLoS One 2014; 9:e100216. [PMID: 24926661 PMCID: PMC4057436 DOI: 10.1371/journal.pone.0100216] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 05/23/2014] [Indexed: 02/07/2023] Open
Abstract
Nuclear apoptosis-inducing factor 1 (NAIF1) was previously reported to induce apoptosis. Moreover, the expression of NAIF1 was significantly down-regulated in human gastric cancer tissues compared to adjacent normal tissues. However, the mechanism by which the NAIF1 gene induces apoptosis is not fully understood. Our results show that NAIF1 was minimally expressed in all the tested gastric cancer cell lines. Our data also demonstrates that NAIF1 is localized in the nuclei of cells as detected by monitoring the green fluorescence of NAIF1-GFP fusion protein using fluorescent confocal microscopy. Next, a comparative proteomic approach was used to identify the differential expression of proteins between gastric cancer cell lines MKN45/NAIF1 (−) and MKN45/NAIF1 (+). We found five proteins (proteasome 26S subunit 2, proteasome 26S subunit 13, NADH dehydrogenase Fe-S protein 1, chaperonin containing TCP1 subunit 3 and thioredoxin reductase 1) that were up-regulated and three proteins (ribonuclease inhibitor 1, 14-3-3 protein epsilon isoform and apolipoprotein A-I binding protein) that were down-regulated in the MKN45 cells overexpressing NAIF1. We also discovered that NAIF1 could induce cell cycle arrest at G1/S phase by altering the expression of cell cycle proteins cyclinD1, cdc2 and p21. The differentially expressed proteins identified here are related to various cellular programs involving cell cycle, apoptosis, and signal transduction regulation and suggest that NAIF1 may be a tumor suppressor in gastric cancer. Our research provides evidence that elucidates the role of how NAIF1 functions in gastric cancer.
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Teramoto S, Tsukiyama T, Okumoto Y, Tanisaka T. Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing. PLoS Genet 2014; 10:e1004396. [PMID: 24921928 PMCID: PMC4055405 DOI: 10.1371/journal.pgen.1004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/06/2014] [Indexed: 01/14/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu), mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP), and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP). Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution. Transposable elements are major components of eukaryotic genomes, comprising a large portion of the genome in some species. Miniature inverted-repeat transposable elements (MITEs), which belong to the class II DNA transposable elements, are abundant in gene-rich regions, and their copy numbers are very high; therefore, they have been considered to contribute to genome evolution. Because MITEs are short and have no coding capacity, they cannot transpose their positions without the aid of transposase, provided in trans by their autonomous element(s). It has been unknown how MITEs amplify themselves to high copy numbers in the genome. Our results demonstrate that the rice active MITE mPing is mobilized in the embryo by the developmental stage-specific up-regulation of an autonomous element, Ping, and thereby successfully amplifies itself to a high copy number in the genome. The short-term expression of Ping is thought to be a strategy of the mPing family for amplifying mPing by escaping the silencing mechanism of the host genome.
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Affiliation(s)
- Shota Teramoto
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, Japan
| | - Takuji Tsukiyama
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, Japan
- * E-mail:
| | - Yutaka Okumoto
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, Japan
| | - Takatoshi Tanisaka
- Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, Japan
- Department of Agriculture for Regional Reclamation, Kibi International University, Minami-Awaji, Japan
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Fu Q, Shi H, Shi M, Meng L, Zhang H, Ren Y, Guo F, Jia B, Wang P, Ni W, Chen C. bta-miR-29b attenuates apoptosis by directly targeting caspase-7 and NAIF1 and suppresses bovine viral diarrhea virus replication in MDBK cells. Can J Microbiol 2014; 60:455-60. [PMID: 24965127 DOI: 10.1139/cjm-2014-0277] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
MicroRNAs (miRNAs) are small, endogenous, noncoding RNA molecules that serve as powerful regulators of multiple cellular processes, including apoptosis, differentiation, growth, and proliferation. Bovine viral diarrhea virus (BVDV) contributes significantly to health-related economic losses in the beef and dairy industries. Although BVDV-induced apoptosis correlates with increased intracellular viral RNA accumulation and with bta-miR-29b (miR-29b) expression upregulation in Madin-Darby bovine kidney (MDBK) cells infected with BVDV strain NADL, the role of miR-29b in regulating BVDV-infection-related apoptosis remains unexplored. Here, we report that miR-29b serves as a new miRNA regulating apoptosis. We showed that miR-29b target sequences were present in the 3' untranslated regions of 2 key apoptosis regulators mRNAs, cysteine aspartases-7 (caspase-7) and nuclear apoptosis-inducing factor 1 (NAIF1). Indeed, upon miRNA overexpression, both mRNA and protein levels of caspase-7 and NAIF1 were decreased. We further found that miR-29b attenuated apoptosis by directly regulating intracellular levels of caspase-7 and NAIF1. Moreover, apoptosis blockage by miR-29b was rescued upon co-infection of MDBK cells with lentiviruses expressing caspase-7 and NAIF1. Importantly, miR-29b decreased BVDV NADL envelope glycoprotein E1 mRNA levels and suppressed viral replication. These studies advance our understanding of the mechanisms of miRNAs in mediating the cells combating viral infections.
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Affiliation(s)
- Qiang Fu
- a College of Animal Science and Technology, Shihezi University, Shihezi 832003, Xinjiang, People's Republic of China
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Park KC, Son JH, Lee SII, Kim KS, Chang YS, Kim NS. Pong-like elements in Arabidopsis and Brassica rapa: its regulation of F-box protein gene in different ecotypes of Arabidopsis thaliana. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Arnaoty A, Gouilleux-Gruart V, Casteret S, Pitard B, Bigot Y, Lecomte T. Reliability of the nanopheres-DNA immunization technology to produce polyclonal antibodies directed against human neogenic proteins. Mol Genet Genomics 2013; 288:347-63. [DOI: 10.1007/s00438-013-0754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 03/11/2013] [Indexed: 10/26/2022]
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Jursch T, Miskey C, Izsvák Z, Ivics Z. Regulation of DNA transposition by CpG methylation and chromatin structure in human cells. Mob DNA 2013; 4:15. [PMID: 23676100 PMCID: PMC3680223 DOI: 10.1186/1759-8753-4-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/19/2013] [Indexed: 12/25/2022] Open
Abstract
Background The activity of transposable elements can be regulated by different means. DNA CpG methylation is known to decrease or inhibit transpositional activity of diverse transposons. However, very surprisingly, it was previously shown that CpG methylation of the Sleeping Beauty (SB) transposon significantly enhanced transposition in mouse embryonic stem cells. Results In order to investigate the unexpected response of SB transposition to CpG methylation, related transposons from the Tc1/mariner superfamily, that is, Tc1, Himar1, Hsmar1, Frog Prince (FP) and Minos were tested to see how transposition was affected by CpG methylation. A significant increase of >20-fold in transposition of SB, FP and Minos was seen, whereas Tc1, Himar1 and Hsmar1 showed no difference in transposition upon CpG-methylation. The terminal inverted repeats (TIRs) of the SB, FP and Minos elements share a common structure, in which each TIR contains two functionally important binding sites for the transposase (termed the IR/DR structure). The group of IR/DR elements showed increased excision after CpG methylation compared to untreated transposon donor plasmids. We found that de novo CpG methylation is not required for transposition. A mutated FP donor plasmid with depleted CpG sites in both TIRs was as efficient in transposition as the wild-type transposon, indicating that CpG sites inside the TIRs are not responsible for altered binding of factors potentially modulating transposition. By using an in vivo one-hybrid DNA-binding assay in cultured human cells we found that CpG methylation had no appreciable effect on the affinity of SB transposase to its binding sites. However, chromatin immunoprecipitation indicated that CpG-methylated transposon donor plasmids are associated with a condensed chromatin structure characterized by trimethylated histone H3K9. Finally, DNA compaction by protamine was found to enhance SB transposition. Conclusions We have shown that DNA CpG methylation upregulates transposition of IR/DR elements in the Tc1/mariner superfamily. CpG methylation provokes the formation of a tight chromatin structure at the transposon DNA, likely aiding the formation of a catalytically active complex by facilitating synapsis of sites bound by the transposase.
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Affiliation(s)
- Tobias Jursch
- Max Delbrück Center for Molecular Medicine, D-13125, Berlin, Germany.
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Pereira JF, Almeida APMM, Cota J, Pamphile JA, Ferreira da Silva G, de Araújo EF, Gramacho KP, Brommonschenkel SH, Pereira GAG, de Queiroz MV. Boto, a class II transposon in Moniliophthora perniciosa, is the first representative of the PIF/Harbinger superfamily in a phytopathogenic fungus. Microbiology (Reading) 2013; 159:112-125. [DOI: 10.1099/mic.0.062901-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Jorge Fernando Pereira
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | - Júnio Cota
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - João Alencar Pamphile
- Universidade Estadual de Maringá, Departamento de Biologia Celular e Genética, CEP 87020-900, Maringá, PR, Brazil
| | - Gilvan Ferreira da Silva
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - Elza Fernandes de Araújo
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | | | | | - Marisa Vieira de Queiroz
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
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39
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Transposable elements domesticated and neofunctionalized by eukaryotic genomes. Plasmid 2013; 69:1-15. [DOI: 10.1016/j.plasmid.2012.08.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/30/2012] [Accepted: 08/08/2012] [Indexed: 12/21/2022]
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Oh SA, Allen T, Kim GJ, Sidorova A, Borg M, Park SK, Twell D. Arabidopsis Fused kinase and the Kinesin-12 subfamily constitute a signalling module required for phragmoplast expansion. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:550-63. [PMID: 22448600 DOI: 10.1111/j.1365-313x.2012.05007.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The conserved Fused kinase plays vital but divergent roles in many organisms from Hedgehog signalling in Drosophila to polarization and chemotaxis in Dictyostelium. Previously we have shown that Arabidopsis Fused kinase termed TWO-IN-ONE (TIO) is essential for cytokinesis in both sporophytic and gametophytic cell types. Here using in vivo imaging of GFP-tagged microtubules in dividing microspores we show that TIO is required for expansion of the phragmoplast. We identify the phragmoplast-associated kinesins, PAKRP1/Kinesin-12A and PAKRP1L/Kinesin-12B, as TIO-interacting proteins and determine TIO-Kinesin-12 interaction domains and their requirement in male gametophytic cytokinesis. Our results support the role of TIO as a functional protein kinase that interacts with Kinesin-12 subfamily members mainly through the C-terminal ARM repeat domain, but with a contribution from the N-terminal kinase domain. The interaction of TIO with Kinesin proteins and the functional requirement of their interaction domains support the operation of a Fused kinase signalling module in phragmoplast expansion that depends upon conserved structural features in diverse Fused kinases.
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Affiliation(s)
- Sung Aeong Oh
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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Song G, Li Q, Long Y, Hackett PB, Cui Z. Effective Expression-Independent Gene Trapping and Mutagenesis Mediated by Sleeping Beauty Transposon. J Genet Genomics 2012; 39:503-20. [DOI: 10.1016/j.jgg.2012.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 05/21/2012] [Accepted: 05/28/2012] [Indexed: 01/12/2023]
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Effective gene trapping mediated by Sleeping Beauty transposon. PLoS One 2012; 7:e44123. [PMID: 22952894 PMCID: PMC3432063 DOI: 10.1371/journal.pone.0044123] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/30/2012] [Indexed: 01/14/2023] Open
Abstract
Gene trapping is a high-throughput approach to elucidate gene functions by disrupting and recapitulating expression of genes in a target genome. A number of transposon-based gene-trapping systems are developed for mutagenesis in cells and model organisms, but there is still much room for the improvement of their efficiency in gene disruption and mutation. Herein, a gene-trapping system mediated by Sleeping Beauty (SB) transposon was developed by inclusion of three functional cassettes. The mutation cassette can abrogate the splice of trapped genes and terminate their translation. Once an endogenous gene is captured, the finding cassette independently drives the translation of reporter gene in HeLa cells and zebrafish embryos. The efficiency cassette controls the remobilization of integrated traps through inducible expression of SB gene. Analysis of transposon-genome junctions indicate that most of trap cassettes are integrated into an intron without an obvious 3′ bias. The transcription of trapped genes was abrogated by alternative splicing of the mutation cassette. In addition, integrated transposons can be induced to excise from their original insertion sites. Furthermore, the Cre/LoxP system was introduced to delete the efficiency cassette for stabilization of gene interruption and bio-safety. Thus, this gene-trap vector is an alternative and effective tool for the capture and disruption of endogenous genes in vitro and in vivo.
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Ammar I, Gogol-Döring A, Miskey C, Chen W, Cathomen T, Izsvák Z, Ivics Z. Retargeting transposon insertions by the adeno-associated virus Rep protein. Nucleic Acids Res 2012; 40:6693-712. [PMID: 22523082 PMCID: PMC3413126 DOI: 10.1093/nar/gks317] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Sleeping Beauty (SB), piggyBac (PB) and Tol2 transposons are promising instruments for genome engineering. Integration site profiling of SB, PB and Tol2 in human cells showed that PB and Tol2 insertions were enriched in genes, whereas SB insertions were randomly distributed. We aimed to introduce a bias into the target site selection properties of the transposon systems by taking advantage of the locus-specific integration system of adeno-associated virus (AAV). The AAV Rep protein binds to Rep recognition sequences (RRSs) in the human genome, and mediates viral integration into nearby sites. A series of fusion constructs consisting of the N-terminal DNA-binding domain of Rep and the transposases or the N57 domain of SB were generated. A plasmid-based transposition assay showed that Rep/SB yielded a 15-fold enrichment of transposition at a particular site near a targeted RRS. Genome-wide insertion site analysis indicated that an approach based on interactions between the SB transposase and Rep/N57 enriched transgene insertions at RRSs. We also provide evidence of biased insertion of the PB and Tol2 transposons. This study provides a comparative insight into target site selection properties of transposons, as well as proof-of-principle for targeted chromosomal transposition by composite protein–protein and protein–DNA interactions.
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Affiliation(s)
- Ismahen Ammar
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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Swierczek M, Izsvák Z, Ivics Z. The Sleeping Beauty transposon system for clinical applications. Expert Opin Biol Ther 2011; 12:139-53. [PMID: 22176302 DOI: 10.1517/14712598.2012.642358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Extensive efforts have been made to establish efficient and safe gene delivery protocols that could meet demanding expectations of a successful gene therapy. The Sleeping Beauty (SB) transposon system combines simplicity and inexpensive manufacture offered by plasmid-based vector formulation with integrative features exhibited by some viral vectors. Activated after over ten million years of silent genomic existence, the SB transposable element entered the 21st century as a potent technology for a broad range of applications in genome engineering, including gene therapy. Beneficially for gene therapy purposes, the SB system has been demonstrated to enable persistent expression of therapeutic genes followed by restoration of homeostasis in a variety of disease models. Importantly, this non-viral gene delivery vehicle is postulated to constitute a relatively safe vector system, because it lacks a preference for inserting into transcription units and their upstream regulatory regions, thereby minimizing genotoxic risks that might be associated with vector integration. Further evolution and wide, comprehensive preclinical testing of the SB transposon system in the context of several disease models is expected to further refine this valuable technology matched by enhanced biosafety towards disease treatment.
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Affiliation(s)
- Marta Swierczek
- Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, D-63225 Langen, Germany
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Smith JJ, Sumiyama K, Amemiya CT. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol 2011; 29:985-93. [PMID: 22045999 DOI: 10.1093/molbev/msr267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Emerging data from the coelacanth genome are beginning to shed light on the origin and evolution of tetrapod genes and noncoding elements. Of particular relevance is the realization that coelacanth retains active copies of transposable elements that once served as raw material for the evolution of new functional sequences in the vertebrate lineage. Recognizing the evolutionary significance of coelacanth genome in this regard, we employed an ab initio search strategy to further classify its repetitive complement. This analysis uncovered a class of interspersed elements (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to coelacanth genome structure and gene content (∼1% to 4% or the genome). Sequence analyses indicate that 1) each ∼8.7 kb LatiHarb1 element contains two coding regions, a transposase gene and a gene whose function is as yet unknown (MYB-like) and 2) copies of LatiHarb1 retain biological activity in the coelacanth genome. Functional analyses verify transcriptional and enhancer activities of LatiHarb1 in vivo and reveal transcriptional decoupling that could permit MYB-like genes to play functional roles not directly linked to transposition. Thus, LatiHarb1 represents the first known instance of a harbinger-superfamily transposon with contemporary activity in a vertebrate genome. Analyses of LatiHarb1 further corroborate the notion that exaptation of anciently active harbinger elements gave rise to at least two vertebrate genes (harbi1 and naif1) and indicate that the vertebrate gene tsnare1 also traces its ancestry to this transposon superfamily. Based on our analyses of LatiHarb1, we speculate that several functional features of harbinger elements may predispose the transposon superfamily toward recurrent exaptive evolution of cellular coding genes. In addition, these analyses further reinforce the broad utility of the coelacanth genome and other "outgroup" genomes in understanding the ancestry and evolution of vertebrate genes and genomes.
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Affiliation(s)
- Jeramiah J Smith
- Benaroya Research Institute at Virginia Mason Medical Center, Seattle, WA, USA.
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Demattei MV, Hedhili S, Sinzelle L, Bressac C, Casteret S, Moiré N, Cambefort J, Thomas X, Pollet N, Gantet P, Bigot Y. Nuclear importation of Mariner transposases among eukaryotes: motif requirements and homo-protein interactions. PLoS One 2011; 6:e23693. [PMID: 21876763 PMCID: PMC3158080 DOI: 10.1371/journal.pone.0023693] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 07/22/2011] [Indexed: 12/13/2022] Open
Abstract
Mariner-like elements (MLEs) are widespread transposable elements in animal genomes. They have been divided into at least five sub-families with differing host ranges. We investigated whether the ability of transposases encoded by Mos1, Himar1 and Mcmar1 to be actively imported into nuclei varies between host belonging to different eukaryotic taxa. Our findings demonstrate that nuclear importation could restrict the host range of some MLEs in certain eukaryotic lineages, depending on their expression level. We then focused on the nuclear localization signal (NLS) in these proteins, and showed that the first 175 N-terminal residues in the three transposases were required for nuclear importation. We found that two components are involved in the nuclear importation of the Mos1 transposase: an SV40 NLS-like motif (position: aa 168 to 174), and a dimerization sub-domain located within the first 80 residues. Sequence analyses revealed that the dimerization moiety is conserved among MLE transposases, but the Himar1 and Mcmar1 transposases do not contain any conserved NLS motif. This suggests that other NLS-like motifs must intervene in these proteins. Finally, we showed that the over-expression of the Mos1 transposase prevents its nuclear importation in HeLa cells, due to the assembly of transposase aggregates in the cytoplasm.
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Affiliation(s)
| | - Sabah Hedhili
- CIRAD, UMR 1098 Développement et Amélioration des Plantes, Montpellier, France
| | - Ludivine Sinzelle
- Metamorphosys, CNRS UPS3201-Université d'Evry Val d'Essonne, Genavenir 3 - Genopole Campus 1, Evry, France
| | | | - Sophie Casteret
- PRC, UMR INRA-CNRS 6175, Nouzilly, France
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | | | - Jeanne Cambefort
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | - Xavier Thomas
- GICC, UMR CNRS 6239, UFR des Sciences et Techniques, Tours, France
| | - Nicolas Pollet
- Metamorphosys, CNRS UPS3201-Université d'Evry Val d'Essonne, Genavenir 3 - Genopole Campus 1, Evry, France
| | - Pascal Gantet
- CIRAD, UMR 1098 Développement et Amélioration des Plantes, Montpellier, France
| | - Yves Bigot
- PRC, UMR INRA-CNRS 6175, Nouzilly, France
- * E-mail:
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Ivics Z, Izsvák Z. The expanding universe of transposon technologies for gene and cell engineering. Mob DNA 2010; 1:25. [PMID: 21138556 PMCID: PMC3016246 DOI: 10.1186/1759-8753-1-25] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 12/07/2010] [Indexed: 12/16/2022] Open
Abstract
Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion. The mobility of class II transposable elements (DNA transposons) can be controlled by conditionally providing the transposase component of the transposition reaction. Thus, a DNA of interest (be it a fluorescent marker, a small hairpin (sh)RNA expression cassette, a mutagenic gene trap or a therapeutic gene construct) cloned between the inverted repeat sequences of a transposon-based vector can be used for stable genomic insertion in a regulated and highly efficient manner. This methodological paradigm opened up a number of avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture, the production of germline transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species, and therapy of genetic disorders in humans. Sleeping Beauty (SB) was the first transposon shown to be capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering including transgenesis, insertional mutagenesis, and therapeutic somatic gene transfer both ex vivo and in vivo. The first clinical application of the SB system will help to validate both the safety and efficacy of this approach. In this review, we describe the major transposon systems currently available (with special emphasis on SB), discuss the various parameters and considerations pertinent to their experimental use, and highlight the state of the art in transposon technology in diverse genetic applications.
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Affiliation(s)
- Zoltán Ivics
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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48
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Hickman AB, Chandler M, Dyda F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 2010; 45:50-69. [PMID: 20067338 DOI: 10.3109/10409230903505596] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA rearrangements are important in genome function and evolution. Genetic material can be rearranged inadvertently during processes such as DNA repair, or can be moved in a controlled manner by enzymes specifically dedicated to the task. DNA transposases comprise one class of such enzymes. These move DNA segments known as transposons to new locations, without the need for sequence homology between transposon and target site. Several biochemically distinct pathways have evolved for DNA transposition, and genetic and biochemical studies have provided valuable insights into many of these. However, structural information on transposases - particularly with DNA substrates - has proven elusive in most cases. On the other hand, large-scale genome sequencing projects have led to an explosion in the number of annotated prokaryotic and eukaryotic mobile elements. Here, we briefly review biochemical and mechanistic aspects of DNA transposition, and propose that integrating sequence information with structural information using bioinformatics tools such as secondary structure prediction and protein threading can lead not only to an additional level of understanding but possibly also to testable hypotheses regarding transposition mechanisms. Detailed understanding of transposition pathways is a prerequisite for the long-term goal of exploiting DNA transposons as genetic tools and as a basis for genetic medical applications.
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Affiliation(s)
- Alison Burgess Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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Hancock CN, Zhang F, Wessler SR. Transposition of the Tourist-MITE mPing in yeast: an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily. Mob DNA 2010; 1:5. [PMID: 20226077 PMCID: PMC2836001 DOI: 10.1186/1759-8753-1-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 02/01/2010] [Indexed: 12/25/2022] Open
Abstract
Background PIF/Harbinger is the most recently discovered DNA transposon superfamily and is now known to populate genomes from fungi to plants to animals. Mobilization of superfamily members requires two separate element-encoded proteins (ORF1 and TPase). Members of this superfamily also mobilize Tourist-like miniature inverted repeat transposable elements (MITEs), which are the most abundant transposable elements associated with the genes of plants, especially the cereal grasses. The phylogenetic analysis of many plant genomes indicates that MITEs can amplify rapidly from one or a few elements to hundreds or thousands. The most active DNA transposon identified to date in plants or animals is mPing, a rice Tourist-like MITE that is a deletion derivative of the autonomous Ping element. Ping and the closely related Pong are the only known naturally active PIF/Harbinger elements. Some rice strains accumulate ~40 new mPing insertions per plant per generation. In this study we report the development of a yeast transposition assay as a first step in deciphering the mechanism underlying the amplification of Tourist-MITEs. Results The ORF1 and TPase proteins encoded by Ping and Pong have been shown to mobilize mPing in rice and in transgenic Arabidopsis. Initial tests of the native proteins in a yeast assay resulted in very low transposition. Significantly higher activities were obtained by mutation of a putative nuclear export signal (NES) in the TPase that increased the amount of TPase in the nucleus. When introduced into Arabidopsis, the NES mutant protein also catalyzed higher frequencies of mPing excision from the gfp reporter gene. Our yeast assay retains key features of excision and insertion of mPing including precise excision, extended insertion sequence preference, and a requirement for two proteins that can come from either Ping or Pong or both elements. Conclusions The yeast transposition assay provides a robust platform for analysis of the mechanism underlying transposition catalyzed by the two proteins of PIF/Harbinger elements. It recapitulates all of the features of excision and reinsertion of mPing as seen in plant systems. Furthermore, a mutation of a putative NES in the TPase increased transposition both in yeast and plants.
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Affiliation(s)
- C Nathan Hancock
- Plant Biology Department, University of Georgia, Athens, GA 30602, USA.
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