Abstract
BackgroundThe mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved.ResultsWe show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A. lyrata and A. thaliana. Heat-responsiveness of COPIA families is correlated with the presence of putative high affinity heat shock factor binding HREs within their long terminal repeats in seven Brassicaceae species. The strong HRE of ONSEN is conserved over millions of years and has evolved by duplication of a proto-HRE sequence, which was already present early in the evolution of the Brassicaceae. However, HREs of most families are species-specific, and in Boechera stricta, the ONSEN HRE accumulated mutations and lost heat-responsiveness.ConclusionsGain of HREs does not always provide an ultimate selective advantage for TEs, but may increase the probability of their long-term survival during the co-evolution of hosts and genomic parasites.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1072-3) contains supplementary material, which is available to authorized users.
Highlights
The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms
We found only 2.9 % (n = 980) of genes still upregulated in A. lyrata and 0.6 % (n = 192) in A. thaliana
Search in other species revealed the presence of COPIA37 in B. rapa (n = 2), C. rubella (n = 2), and E. salsugineum (n = 2; Table 1), but here we found only low affinity binding gap and/or step heat-responsive elements (HREs) in the latter two species (Fig. 3a; Additional file 5: Figure S6)
Summary
The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. It remains unknown whether this is a common and potentially conserved trait and how it has evolved. Plants evolved several layers of sophisticated epigenetic silencing mechanisms in order to suppress TE activity. Their transcripts are degraded by the post-transcriptional gene silencing (PTGS) pathway, which greatly reduces possible transposition events [4]. In addition to the nimble epigenetic silencing system, entire TEs can be physically removed from the host genome by deletion-biased homologous recombination processes [10]
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