Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for muc...
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| Format: | Article |
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MDPI AG
2023-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/5/1101 |
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| author | Joseph L. Pegler Jackson M. J. Oultram Christopher W. G. Mann Bernard J. Carroll Christopher P. L. Grof Andrew L. Eamens |
| author_facet | Joseph L. Pegler Jackson M. J. Oultram Christopher W. G. Mann Bernard J. Carroll Christopher P. L. Grof Andrew L. Eamens |
| author_sort | Joseph L. Pegler |
| collection | DOAJ |
| description | Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms. |
| first_indexed | 2024-03-11T07:13:54Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-11T07:13:54Z |
| publishDate | 2023-03-01 |
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| series | Plants |
| spelling | doaj.art-b50932ac94514412a9beaf17ae6e75e82023-11-17T08:24:08ZengMDPI AGPlants2223-77472023-03-01125110110.3390/plants12051101Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene EvolutionJoseph L. Pegler0Jackson M. J. Oultram1Christopher W. G. Mann2Bernard J. Carroll3Christopher P. L. Grof4Andrew L. Eamens5Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, AustraliaCentre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, AustraliaSchool of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, AustraliaSchool of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, AustraliaCentre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, AustraliaSchool of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, AustraliaAngiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.https://www.mdpi.com/2223-7747/12/5/1101angiospermstransposable element (TE)miniature inverted-repeat transposable element (MITE)RNA-directed DNA methylation (RdDM)repeat-associated small-interfering RNA (rasiRNA)microRNA (miRNA) |
| spellingShingle | Joseph L. Pegler Jackson M. J. Oultram Christopher W. G. Mann Bernard J. Carroll Christopher P. L. Grof Andrew L. Eamens Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution Plants angiosperms transposable element (TE) miniature inverted-repeat transposable element (MITE) RNA-directed DNA methylation (RdDM) repeat-associated small-interfering RNA (rasiRNA) microRNA (miRNA) |
| title | Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution |
| title_full | Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution |
| title_fullStr | Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution |
| title_full_unstemmed | Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution |
| title_short | Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant <i>MICRORNA</i> Gene Evolution |
| title_sort | miniature inverted repeat transposable elements small dna transposons that have contributed to plant i microrna i gene evolution |
| topic | angiosperms transposable element (TE) miniature inverted-repeat transposable element (MITE) RNA-directed DNA methylation (RdDM) repeat-associated small-interfering RNA (rasiRNA) microRNA (miRNA) |
| url | https://www.mdpi.com/2223-7747/12/5/1101 |
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