Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture

Masuta, Yukari; Nozawa, Kohei; Takagi, Hiroki; Yaegashi, Hiroki; Tanaka, Keisuke; Ito, Tasuku; Saito, Hideyuki; Kobayashi, Hisato; Matsunaga, Wataru; Masuda, Seiji; Kato, Atsushi; Ito, Hidetaka

doi:10.1093/pcp/pcw202

Cited by 19 publications

(22 citation statements)

References 47 publications

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“…In the plant genome, insertional inactivation and other genome rearrangements lead to a wide spectrum of recombination and chromosomal instability (Raskina et al 2008;Belyayev et al 2010;Brueckner et al 2012;Hosid et al 2012). RTE-induced genetic rearrangements can lead to nonallelic homologous recombination (Yu et al 2012;Ben-David et al 2013) or insertional mutagenesis caused by retrotransposons 'hopping' within gene coding sequences; it causes diverse effects on target gene expression, depending on the intragenic location, the orientation, the length of the inserted sequence and other factors, or the activation and mobilisation of small RNAs (Nuthikattu et al 2013;Forestan et al 2017;Masuta et al 2017;Schorn et al 2017). For example, the genes with nearby TE insertions are those most strongly affected by RNA polymerase IV-mediated gene silencing.…”

Section: Epigenetic Control and Retrotransposon Activitymentioning

confidence: 99%

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Kalendar

Amenov

Daniyarov

2019

Functional Plant Biol.

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Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The ‘copy and paste’ lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5ʹ or 3ʹ junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants’ genetic diversity.

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Section: Epigenetic Control and Retrotransposon Activitymentioning

confidence: 99%

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Kalendar

Amenov

Daniyarov

2019

Functional Plant Biol.

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“…When exposed to heat stress, a heat shock factor A2 binds to the HRE and triggers its transcriptional activity. We also found that the heat-activated ONSEN was transposed in a mutant that was deficient in small RNA biosynthesis as well as in plants regenerated from callus [8,10]. Interestingly, in A. thaliana, ONSEN preferentially inserts within the genes [8].…”

Section: Introductionmentioning

confidence: 80%

Epigenetic Regulation of a Heat-Activated Retrotransposon in Cruciferous Vegetables

et al. 2017

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Transposable elements (TEs) are highly abundant in plant genomes. Environmental stress is one of the critical stimuli that activate TEs. We analyzed a heat-activated retrotransposon, named ONSEN, in cruciferous vegetables. Multiple copies of ONSEN-like elements (OLEs) were found in all of the cruciferous vegetables that were analyzed. The copy number of OLE was high in Brassica oleracea, which includes cabbage, cauliflower, broccoli, Brussels sprout, and kale. Phylogenic analysis demonstrated that some OLEs transposed after the allopolyploidization of parental Brassica species. Furthermore, we found that the high copy number of OLEs in B. oleracea appeared to induce transpositional silencing through epigenetic regulation, including DNA methylation. The results of this study would be relevant to the understanding of evolutionary adaptations to thermal environmental stress in different species.

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“…Moreover, we classified the heat-activated ONSEN/ AT5TE15240 as a class B/heterochromatic TE based on its siRNA dynamics, and ONSEN transcription and transposition are greatly enhanced in RdDM-defective mutants [78] . Interestingly, 24-nt siRNAs were increased throughout the body of ONSEN TEs after heat-stress and this was further enhanced in rapidly dividing undifferentiated calli [79] , which has increased chromatin accessibility in rice [79,80] . Based on these results, as well as our previous observation that heat-stress related genes are significantly enriched in preglobular embryos [41] , we suggest that the chromatin dynamics caused by heat-stress and subsequent recovery are analogous to what we observed in early embryos.…”

Section: Discussionmentioning

confidence: 99%

Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis

Papareddy

Páldi

Paulraj

et al. 2020

Preprint

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Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development, and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation in eukaryotes, but little is known about how chromatin regulates siRNA transcription. We demonstrated that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos. Depending on whether they are located in euchromatic or heterochromatic regions of the genome, bipartite-classified TEs generate siRNAs throughout embryogenesis according to two distinct patterns. siRNAs are transcribed in embryos and required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.

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Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture

Cited by 19 publications

References 47 publications

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Epigenetic Regulation of a Heat-Activated Retrotransposon in Cruciferous Vegetables

Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis

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