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Huang F, Qiao X, Mei S, Zhang C, Jiang C. Analysis of non-coding small RNA similarity/sharing between plant and animal genomes. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2437-2440. [PMID: 37481687 DOI: 10.1007/s11427-022-2373-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 05/17/2023] [Indexed: 07/24/2023]
Affiliation(s)
- Fengming Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiangyu Qiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Song Mei
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Cong Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Chengyu Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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Kelleher ES. Jack of all trades versus master of one: how generalist versus specialist strategies of transposable elements relate to their horizontal transfer between lineages. Curr Opin Genet Dev 2023; 81:102080. [PMID: 37459818 PMCID: PMC11062761 DOI: 10.1016/j.gde.2023.102080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 08/15/2023]
Abstract
Transposable elements (TEs) are obligate genomic parasites, relying on host germline cells to ensure their replication and passage to future generations. While some TEs exhibit high fidelity to their host genome, being passed from parent to offspring through vertical transmission for millions of years, others frequently invade new and distantly related hosts through horizontal transfer. In this review, I highlight how the complexity of interactions between TE and host required for transposition may be an important determinant of horizontal transfer: with TEs with more complex regulatory requirements being less able to invade new host genomes.
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Affiliation(s)
- Erin S Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.
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Hartig N, Seibt KM, Heitkam T. How to start a LINE: 5' switching rejuvenates LINE retrotransposons in tobacco and related Nicotiana species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36965091 DOI: 10.1111/tpj.16208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
By contrast to their conserved mammalian counterparts, plant long interspersed nuclear elements (LINEs) are highly variable, splitting into many low-copy families. Curiously, LINE families from the retrotransposable element (RTE) clade retain a stronger sequence conservation and hence reach higher copy numbers. The cause of this RTE-typical property is not yet understood, but would help clarify why some transposable elements are removed quickly, whereas others persist in plant genomes. Here, we bring forward a detailed study of RTE LINE structure, diversity and evolution in plants. For this, we argue that the nightshade family is the ideal taxon to follow the evolutionary trajectories of RTE LINEs, given their high abundance, recent activity and partnership to non-autonomous elements. Using bioinformatic, cytogenetic and molecular approaches, we detect 4029 full-length RTE LINEs across the Solanaceae. We finely characterize and manually curate a core group of 458 full-length LINEs in allotetraploid tobacco, show an integration event after polyploidization and trace hybridization by RTE LINE composition of parental genomes. Finally, we reveal the role of the untranslated regions (UTRs) as causes for the unique RTE LINE amplification and evolution pattern in plants. On the one hand, we detected a highly conserved motif at the 3' UTR, suggesting strong selective constraints acting on the RTE terminus. On the other hand, we observed successive rounds of 5' UTR cycling, constantly rejuvenating the promoter sequences. This interplay between exchangeable promoters and conserved LINE bodies and 3' UTR likely allows RTE LINEs to persist and thrive in plant genomes.
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Affiliation(s)
- Nora Hartig
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Tony Heitkam
- Faculty of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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Fambrini M, Usai G, Vangelisti A, Mascagni F, Pugliesi C. The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 2020; 58:e23399. [DOI: 10.1002/dvg.23399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
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