Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

Drongitis, Denise; Aniello, Francesco; Fucci, Laura; Donizetti, Aldo

doi:10.3390/ijms20225755

Cited by 37 publications

(38 citation statements)

References 70 publications

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“…Two types of TEs have been identified based on their transposition mechanisms, namely class I retrotransposons and class II DNA transposons [28]. Retrotransposons are RNA-based TEs which duplicate themselves and move within the genome in a semi-conservative manner through a 'copy-and-paste' mechanism of an RNA intermediate [28][29][30]. DNA transposons, on the other hand, use a conservative style of transposition and move directly by a 'cut-and-paste' mechanism [31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.

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Section: Introductionmentioning

confidence: 99%

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Ramakrishnan

Vinod

et al. 2019

Forests

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“…Such insertions can lead to alterations of gene expression (Bourque et al, 2018; Finnegan, 2012; Zhao et al, 2018). In addition, insertion of a TE into the coding sequence of a gene, particularly within an exon, often results in a complete loss of gene function, with subsequent mutations and drastic changes in the coded protein (Bourque et al, 2018; Drongitis, Aniello, Fucci, & Donizetti, 2019).…”

Section: Insertion Sites Of Tesmentioning

confidence: 99%

“…Despite the occasional selective advantage of TE insertions, the vast majority of TE activities are almost certainly neutral, at best, and harmful at worst (Slotkin & Martienssen, 2007). Hence, it is not surprising that plants and organisms in general spend considerable resources on transposon control (Drongitis et al, 2019; Song & Schaack, 2018). In host genomes, this is largely achieved by various epigenetic silencing mechanisms, which involve histone modifications, DNA methylation, and small RNAs (Jansz, 2019; Koonin et al, 2020; Law & Jacobsen, 2010; Le, Miyazaki, Takuno, & Saze, 2015; Slotkin & Martienssen, 2007; Zhang, Lang, & Zhu, 2018).…”

Section: Epigenetic Regulation Of Tesmentioning

confidence: 99%

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Fambrini

Usai

Vangelisti

et al. 2020

Genesis

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Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.

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“…This overexpression could support the hypothesis that HERVs can be used in comparative studies to find polymorphisms caused by the insertion of these retroelements. Other TEs have been used in comparative studies to find transposon insertion polymorphisms (TIPs) associated with certain biological phenomena, such as the adaptation processes of rice [30], paramutation and gene silencing [31], and gene expression regulation in several organisms [32][33][34].…”

Section: Introductionmentioning

confidence: 99%

TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets

Orozco-Arias

Tobón-Orozco

Piña

et al. 2020

Biology

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Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. A particular type of TE called LTR-retrotransposons comprises almost 8% of the human genome. Among LTR retrotransposons, human endogenous retroviruses (HERVs) bear structural and functional similarities to retroviruses. Several tools allow the detection of transposon insertion polymorphisms (TIPs) but fail to efficiently analyze large genomes or large datasets. Here, we developed a computational tool, named TIP_finder, able to detect mobile element insertions in very large genomes, through high-performance computing (HPC) and parallel programming, using the inference of discordant read pair analysis. TIP_finder inputs are (i) short pair reads such as those obtained by Illumina, (ii) a chromosome-level reference genome sequence, and (iii) a database of consensus TE sequences. The HPC strategy we propose adds scalability and provides a useful tool to analyze huge genomic datasets in a decent running time. TIP_finder accelerates the detection of transposon insertion polymorphisms (TIPs) by up to 55 times in breast cancer datasets and 46 times in cancer-free datasets compared to the fastest available algorithms. TIP_finder applies a validated strategy to find TIPs, accelerates the process through HPC, and addresses the issues of runtime for large-scale analyses in the post-genomic era. TIP_finder version 1.0 is available at https://github.com/simonorozcoarias/TIP_finder.

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Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

Cited by 37 publications

References 70 publications

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets

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