Transposable elements: multifunctional players in the plant genome

Transposable elements: multifunctional players in the plant genome

04 January 2024 | Asmaa H. Hassan, Morad M. Mokhtar and Achraf El Allali
Transposable elements (TEs) are essential components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. They can move within the genome, leading to changes in gene expression and DNA structure. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function, and evolution. This review provides a comprehensive overview of TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology. TEs are classified into two main classes: class I TEs (retrotransposons) and class II TEs (DNA transposons). Class I TEs are transcribed into RNA, which is reverse transcribed into DNA and inserted into a new location in the genome. Class II TEs move through a "cut and paste" process. TEs are further divided into subcategories, including LTR-RTs, non-LTRs, and DIRS. LTR-RTs are active or inactive in the genome, with active elements being autonomous or non-autonomous based on their structure. LTR-RTs consist of two identical LTRs, TSDs, PBS, PPT, Gag, and Pol genes. The Pol gene encodes domains such as reverse transcriptase, RH, IN, and PR. Some LTR-RTs also have an ENV-like protein. In plant genomes, the assignment of LTR-RTs to Copia and Gypsy is based on the order of RT and IN within the Pol region. Satellite DNAs (satDNAs) are tandemly repeated sequences that are often localized in specific regions of the genome, such as centromeres and heterochromatin. SatDNAs are involved in centromere function, chromosome segregation, and genome stability. They are formed by the amplification of fragments of TEs and consist of repeating units known as monomers. SatDNAs may derive from mobile elements, especially transposons and retrotransposons. Longer satDNA monomers often originate from specific regions of retrotransposons, such as LTRs and UTRs. SatDNAs are predominantly located in heterochromatic regions, possibly due to gene-poor domains that allow safe propagation. However, they are actively involved in centromere structure and function, suggesting an interaction between satDNAs and TEs. TEs play a critical role in plantTransposable elements (TEs) are essential components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. They can move within the genome, leading to changes in gene expression and DNA structure. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function, and evolution. This review provides a comprehensive overview of TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology. TEs are classified into two main classes: class I TEs (retrotransposons) and class II TEs (DNA transposons). Class I TEs are transcribed into RNA, which is reverse transcribed into DNA and inserted into a new location in the genome. Class II TEs move through a "cut and paste" process. TEs are further divided into subcategories, including LTR-RTs, non-LTRs, and DIRS. LTR-RTs are active or inactive in the genome, with active elements being autonomous or non-autonomous based on their structure. LTR-RTs consist of two identical LTRs, TSDs, PBS, PPT, Gag, and Pol genes. The Pol gene encodes domains such as reverse transcriptase, RH, IN, and PR. Some LTR-RTs also have an ENV-like protein. In plant genomes, the assignment of LTR-RTs to Copia and Gypsy is based on the order of RT and IN within the Pol region. Satellite DNAs (satDNAs) are tandemly repeated sequences that are often localized in specific regions of the genome, such as centromeres and heterochromatin. SatDNAs are involved in centromere function, chromosome segregation, and genome stability. They are formed by the amplification of fragments of TEs and consist of repeating units known as monomers. SatDNAs may derive from mobile elements, especially transposons and retrotransposons. Longer satDNA monomers often originate from specific regions of retrotransposons, such as LTRs and UTRs. SatDNAs are predominantly located in heterochromatic regions, possibly due to gene-poor domains that allow safe propagation. However, they are actively involved in centromere structure and function, suggesting an interaction between satDNAs and TEs. TEs play a critical role in plant
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