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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. Plants (Basel) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Khan MF, Shrivastava K, Sinha R, Kumar V, Jaitly AK. Genome wide occurrence and insertion preferences of INGI/RIME and SLACS CRE transposable elements in Trypanosoma brucei. Mob Genet Elements 2017; 6:e1240747. [PMID: 28090379 DOI: 10.1080/2159256x.2016.1240747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/18/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022] Open
Abstract
Retrotransposons play significant role in genome remodelling of T. brucei and about 5% of its genome consists of retrotransposons including INGI/RIME elements. INGI is one of the dispersed repetitive elements in T. brucei genome which is found distributed throughout all the chromosomes. SLACS (Spliced Leader Associated Conserved Sequence) however, is more conserved in its nature and lacks the typical poly-distributional pattern of LINE like transposons. We have found total 589 copies of these TEs with only 17.06 % (104 copies out of 589) copies with both ends intact thus showing a majority of truncated copies. Complete SLACS CRE were found only on chromosome 9, whereas, complete INGI/RIME were more ubiquitously distributed. The 50 - 70 bp upstream flanking sequence of these elements shows suitable nucleotide biophysical properties to favor transposition.
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Affiliation(s)
- Mohd Faheem Khan
- Department of Plant Sciences, M.J.P. Rohilkhand University, Bareilly, UP, India; Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Kush Shrivastava
- Division of Animal Genetics, Indian Veterinary Research Institute , Izatnagar, Bareilly, UP, India
| | - Rebeka Sinha
- Dairy Cattle Breeding Division, National Dairy Research Institute , Karnal, Haryana, India
| | - Virendra Kumar
- Department of Plant Sciences, M.J.P. Rohilkhand University , Bareilly, UP, India
| | - A K Jaitly
- Department of Plant Sciences, M.J.P. Rohilkhand University , Bareilly, UP, India
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Zhao P, Li J, Kang H, Wang H, Fan Z, Yin Z, Wang J, Zhang Q, Wang Z, Liu JF. Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs. Sci Rep 2016; 6:18501. [PMID: 26729041 DOI: 10.1038/srep18501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/19/2015] [Indexed: 01/28/2023] Open
Abstract
In this study, we performed a genome-wide SV detection among the genomes of thirteen pigs from diverse Chinese and European originated breeds by next genetation sequencing, and constrcuted a single-nucleotide resolution map involving 56,930 putative SVs. We firstly identified a SV hotspot spanning 35 Mb region on the X chromosome specifically in the genomes of Chinese originated individuals. Further scrutinizing this region by large-scale sequencing data of extra 111 individuals, we obtained the confirmatory evidence on our initial finding. Moreover, thirty five SV-related genes within the hotspot region, being of importance for reproduction ability, rendered significant different evolution rates between Chinese and European originated breeds. The SV hotspot identified herein offers a novel evidence for assessing phylogenetic relationships, as well as likely explains the genetic difference of corresponding phenotypes and features, among Chinese and European pig breeds. Furthermore, we employed various SVs to infer genetic structure of individuls surveyed. We found SVs can clearly detect the difference of genetic background among individuals. This clues us that genome-wide SVs can capture majority of geneic variation and be applied into cladistic analyses. Characterizing whole genome SVs demonstrated that SVs are significantly enriched/depleted with various genomic features.
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Schwichtenberg K, Wenke T, Zakrzewski F, Seibt KM, Minoche A, Dohm JC, Weisshaar B, Himmelbauer H, Schmidt T. Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species. Plant J 2016; 85:229-44. [PMID: 26676716 DOI: 10.1111/tpj.13103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
Short interspersed nuclear elements (SINEs) are non-autonomous non-long terminal repeat retrotransposons which are widely distributed in eukaryotic organisms. While SINEs have been intensively studied in animals, only limited information is available about plant SINEs. We analysed 22 SINE families from seven genomes of the Amaranthaceae family and identified 34 806 SINEs, including 19 549 full-length copies. With the focus on sugar beet (Beta vulgaris), we performed a comparative analysis of the diversity, genomic and chromosomal organization and the methylation of SINEs to provide a detailed insight into the evolution and age of Amaranthaceae SINEs. The lengths of consensus sequences of SINEs range from 113 nucleotides (nt) up to 224 nt. The SINEs show dispersed distribution on all chromosomes but were found with higher incidence in subterminal euchromatic chromosome regions. The methylation of SINEs is increased compared with their flanking regions, and the strongest effect is visible for cytosines in the CHH context, indicating an involvement of asymmetric methylation in the silencing of SINEs.
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Affiliation(s)
| | - Torsten Wenke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Falk Zakrzewski
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Kathrin M Seibt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - André Minoche
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia
| | - Juliane C Dohm
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Bernd Weisshaar
- CeBiTec & Department of Biology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Heinz Himmelbauer
- Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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Yasuda K, Ito M, Sugita T, Tsukiyama T, Saito H, Naito K, Teraishi M, Tanisaka T, Okumoto Y. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Mol Breed 2013; 32:505-516. [PMID: 24078785 PMCID: PMC3782648 DOI: 10.1007/s11032-013-9885-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/06/2013] [Indexed: 05/02/2023]
Abstract
Transposable elements (TEs) are DNA fragments that have the ability to move from one chromosomal location to another. The insertion of TEs into gene-rich regions often affects changes in the expression of neighboring genes. Miniature Ping (mPing) is an active miniature inverted-repeat TE discovered in the rice genome. It has been found to show exceptionally active transposition in a few japonica rice varieties, including Gimbozu, where mPing insertion rendered adjacent genes stress-inducible. In the Gimbozu population, it is highly possible that several genes with modified expression profiles are segregating due to the de novo mPing insertions. In our study, we utilized a screening system for detecting de novo mPing insertions in the upstream region of target genes and evaluated the effect of mPing on the stress response of the target genes. Screening for 17 targeted genes revealed five genes with the mPing insertion in their promoters. In most cases, the alteration of gene expression was observed under stress conditions, and there was no change in the expression levels of those five genes under normal conditions. These results indicate that the mPing insertion can be used as a genetic tool to modify an expression pattern of a target gene under stress conditions without changing the expression profiles of those under natural conditions.
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Affiliation(s)
- Kanako Yasuda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Makoto Ito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomohiko Sugita
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takuji Tsukiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Ken Naito
- Genebank, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602 Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takatoshi Tanisaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Yutaka Okumoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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