Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae

Ito, Hidetaka; Yoshida, Takanori; Tsukahara, Sayuri; Kawabe, Akira

doi:10.1016/j.gene.2013.01.034

Cited by 67 publications

(57 citation statements)

References 27 publications

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“…All the cruciferous vegetables analyzed in this study have a conserved element that was homologous with a heat-activated retrotransposon in Arabidopsis, named ONSEN. We previously reported that ONSEN related copies were found in the cross-related species of Brassicaceae, forming a cluster with each species in the phylogenetic tree [22]. This study demonstrated that OLEs were conserved among the more distant species.…”

Section: Discussionsupporting

confidence: 53%

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

Nozawa¹,

Kawagishi²,

Kawabe³

et al. 2017

Preprint

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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. The multiple copies of ONSEN-like elements (OLEs) were found in all the cruciferous vegetables that were analyzed. The copy number of OLE was abundant 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 increasing number of OLEs in B. oleracea appeared to be induced transpositional silencing by 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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Section: Discussionsupporting

confidence: 53%

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

Nozawa¹,

Kawagishi²,

Kawabe³

et al. 2017

Preprint

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“…Stress-induced transposon activation has been confirmed by molecular data in many different hosts141819. Therefore, it was necessary to investigate the overlapping information between the identified DMRs and TEs.…”

Section: Resultsmentioning

confidence: 96%

Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas

Huang

Sun

et al. 2016

Sci Rep

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Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs. T0 DRGs, which suggested that 32 °C might be a more intense external stimulus than 18 °C resulting in more changes in the DNA methylation status of cultured microspores. Additionally, 32 °C treatment for 6 h led to increased CHG differential methylations of transposons (DMTs), which were mainly constituted by overlaps between the hypomethylated differentially methylated regions (hypo-DMRs) and transposon elements (TEs). Further analysis demonstrated that the DRGs and their paralogs exhibited differential methylated/demethylated patterns. To summarize, the present study is the first methylome analysis of cultured microspores in response to STHS and may provide valuable information on the roles of DNA methylation in heat response.

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“…Some TEs exhibit stress-responsive transcription or movement [20]- [25]. For example, expression of the tobacco Tnt1 element can be induced by biotic and abiotic stress [22]- [23].…”

Section: Introductionmentioning

confidence: 99%

Transposable elements contribute to activation of maize genes in response to abiotic stress

Makarevitch

Waters

West

et al. 2014

Preprint

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Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as ''junk'' DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up-or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive upregulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

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Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae

Cited by 67 publications

References 27 publications

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas

Transposable elements contribute to activation of maize genes in response to abiotic stress

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