Maize Genomics and Genetics 2024, Vol.15, No.3, 123-135 http://cropscipublisher.com/index.php/mgg 126 Figure 2 TEs as ‘molecular parasites’ or ‘functional symbionts’ (Adopted from Romano and Fanti, 2022) Image caption: As ‘molecular parasites’ TEs can produce a variety of detrimental effects on the host genome. (a) The insertion of TEs within coding exons can cause frame shift mutations disrupting protein sequence and function. (b) TEs can cause genomic instability being the substrate for chromosome rearrangements, such as duplications, deletions, inversions and translocations. (c) The insertions of TEs in regulatory stretches such as in 50 or 30 regions or introns can cause epigenetic modifications resulting in inappropriate activation or repression of gene expression. The co-option of TEs by the host genome may generate new regulatory signals or coding sequences. This process is referred to as ‘molecular domestication’. (d) TEs may contribute new enhancer sequences for transcription factors (grey circle) changing the spatial/temporal regulation of gene expression. (e) After the loss of telomerase, retrotransposons can actively participate in the maintenance of telomeres. Three non-LTR families, HeT-A, TAHRE, and TART form a head-to-tail array. They express Gag and Reverse Transcriptase proteins that are necessary for the elongation of telomeres. (f) TEs can contribute to the maintenance of genome architecture by providing binding sites for the CTCF protein that is responsible for establishing “topologically associated domains” (TADs) (Adopted from Romano and Fanti, 2022) 4 TEs and Genetic Diversity 4.1 Creation of genetic variation through TE insertions and excisions Transposable elements (TEs) are a significant source of genetic variation in maize, contributing to both the structure and function of the genome. TEs can create genetic diversity through their ability to insert and excise themselves within the genome. This process can lead to mutations, gene duplications, and the creation of new regulatory elements, all of which can have profound effects on gene expression and phenotype. The maize genome is particularly rich in TEs, with more than 85% of its sequence attributed to past transposition events (Stitzer et al., 2019). This high TE content has been shown to play a crucial role in shaping the genome's structure and function. For instance, TEs can insert themselves into or near genes, potentially disrupting gene function or altering gene expression patterns. These insertions can be beneficial, neutral, or deleterious, depending on their location and the genes they affect (Figure 3) (Qiu et al., 2021). TEs can also excise themselves from the genome, a process that can restore gene function if the TE was previously disruptive. However, excision is not always precise and can leave behind small insertions or deletions, further contributing to genetic variation. The dynamic nature of TE insertions and excisions thus provides a continuous source of genetic diversity, which can be acted upon by natural selection (Vicient and Casacuberta, 2017).
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