Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

Abstract

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Transcriptome-wide Identification and Expression Analysis of Brachypodium distachyon Transposons in Response to Viral Infection

“…There is a garnering support that genome and transcriptome orientation via transposon activity might have a role in adaptation and regulation of host stress response (Negi et al, 2016). Besides, regulation of epigenetic mechanisms has an impact on transcriptional activity of TEs in the pathogen infection (Yu et al, 2013;Zhu et al, 2016).…”

“…They have long been assumed as "silent, "junk" or "selfish" DNA; however, recent studies have revealed that most of these repetitive sequences have potential roles in affecting host gene regulation and genomic rearrangements (Lisch, 2013;Ito et al, 2016). In addition several studies have shown that under abiotic or biotic stress TEs are activated or transcribed (Negi et al, 2016). Infections by viruses are one of the main biotic stress types for plants to cope with.…”

Emerging roles of chromatin in the maintenance of genome organization and function in plants

“…TEs are genomic elements that must be maintained in a silenced and heterochromatic state in most plant tissues, developmental stages, and growth conditions [24, 25]. The constitutive heterochromatic regions are located at the pericentromeric sites, at telomeres, and in the nucleolus organizing regions [26–28].…”

Viral fitness determines the magnitude of transcriptomic and epigenomic reprogramming of defense responses in plants

“…The mechanism, therefore, establishes a heterochromatin-like environment within the euchromatin. Environmental stresses may pose a challenge for the maintenance of this chromatin border, as genes and TEs can mutually influence their expression under certain conditions (Negi et al, 2016). Changes in cytosine DNA methylation patterns due to stress have also been reported .…”