Contribution of transposable elements in the plant's genome

Abstract

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.

Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators

“…In addition to the 84,482 bp deletion, another large deletion of 13,084 bp, a transposition and a transversion were identified on chromosome 7 of dwarfed plants in comparison to the 12X.v2 genomic sequence. It is known that active mobile elements can cause chromosomal rearrangements, including genomic deletion [43]. Although partial direct repeats were identified near the deletion junction regions by in silico analysis, it is not clear whether they were involved in the formation of deletions.…”

The role of transposable elements in the ecological morphogenesis under the influence of stress

“…Important sources of these non-coding RNAs are TE (Li et al, 2011;Kapusta et al, 2013;Lorenzetti et al, 2016;Cho, 2018). That is, in the course of evolution, TE acquired the ability of self-regulation by the products of processing their own transcripts, which is important in controlling the functioning of genes in cis and in trans (de Souza et al, 2013) and through site-specific transpositions (Markel, 2008;Sahebi et al, 2018).…”

“…As stress signals affecting the activity of certain TE, there may be changes in the intracellular environment during successive cell divisions, starting with the first division of the zygote. The specific composition and distribution of TE for each species suggests that activation of certain TE may cause activation of some BCG by cis and trans regulation (de Souza et al, 2013;Sahebi et al, 2018) and silencing of other BCG via ncRNA formed by processing TE transcripts (Gim et al, 2014;Cho, 2018). As a result, a cascade of sequential changes in BCG expression necessary for cell differentiation may form.…”

“…In addition, TEs can alter the expression of specific genes using ncRNA (Cho, 2018). TEs can act as stress-sensitive regulators, affecting in cis and in trans the functioning of BCG (de Souza et al, 2013;Sahebi et al, 2018). In the course of evolution, host genomes have developed the ability to regulate the activity and specificity of integration for TE.…”

Root-Specific Expression of a Jacalin Lectin Family Protein Gene Requires a Transposable Element Sequence in the Promoter

“…Class II TEs are DNA transposons that use DNA intermediates to transpose via the mechanism known as “cut and paste”. TEs comprise a large proportion of the plant genome, ranging from around 18% in Arabidopsis to nearly 85% in maize [ 1 , 2 ]. Apart from changes to genome size, active TE transpositions can change gene and genome structures through transposition, insertion, excision, chromosome breakage, and ectopic recombination.…”