Transposable Elements and Epigenetic Mechanism: Implications and Their Significance in Crop Improvement

An understanding of the dynamic potential of the genetic material in living organisms is largely a consequence of the discovery and genetic characterization of plant transposable elements. Repeated DNA sequences makes up a large fraction of a typical mammalian genome and some repetitive elements are able to move within the genome i.e. transposons and retrotransposons. DNA transposons move from one genomic location to another by either copy- and paste or cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As a genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens and even contribute to gene therapy. To understand the impact of transposable elements (TEs) and their importance in host genome evolution, it is essential to study TE epigenetic variation in natural population. Concurrent with these significant developments, “epigenetics” is the study of heritable changes in the pattern of gene expression resulting from the modification of DNA bases, histone proteins or non-coding-RNA biogenesis without altering the underlying nucleotide sequence. It provides a better understanding of how epigenetic mechanisms regulate plant transposons. One of the common mechanisms involved in epigenetic changes is methylation of 5th carbon in the nitrogenous base by the action of the enzyme DNA methyltransferase enzyme. In addition, histone proteins are post-translationally modified which may affect transcription, DNA replication, chromosome segregation/condensation and DNA repair process. Small-RNA (particularly small-interfering RNAs) plays a crucial role in DNA methylation via RNA-directed DNA methylation (RdDM) pathway. The epigenetic changes in plants induced by aforesaid processes can be inherited over the generations in the form of epialleles. A detailed understanding of salient epigenetic mechanisms, such as DNA methylation, paramutation, genomic imprinting and gene silencing, leads to practical solutions and novel strategies for future plant improvement programmes. Therefore, the purpose of this review is to highlight the significance and implications of transposon function and major epigenetic phenomena in relation to genome evolution, gene regulation and crop improvement.