Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics

Ramos, Kenneth S.; Bojang, Pasano; Bowers, Emma C.

doi:10.1177/15353702211031247

Cited by 10 publications

(10 citation statements)

References 189 publications

(259 reference statements)

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“…2, 3, 4), which was possibly responsible for stronger progressiveness of Lmb V23.1.3. The LINE element was the most active transposon in human genomes (Ramos et al 2021), participating in regulation of telomere structure, and leading to malignant cell proliferation (Mueller et al 2018) and tumor formation. Therefore, we speculated that the LINE elements in Lmb V23.1.3 could maintain telomere structure of genome, producing unlimited cell proliferation, and resulting in stronger pathogenicity.…”

Section: Size Proportion Counts Of Various Transposons Of Blackleg Ca...mentioning

confidence: 99%

Genome transposon analysis of blackleg causal pathogen

Tian,

Hao,

et al. 2024

Preprint

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Background To understand genome transposon presence of blackleg pathogen and the relationship between its pathogenicity and transposons, we performed transposon analysis of blackleg pathogen through bioinformatics. Results For three pathogen strains, their genome transposon proportion was distantly beyond 4%, the pathogen strain Lmb V23.1.3 indicated the most genome transposons, followed by Lbb B3.5 and Lbb CA1, the LTR retrotransposons proportion was obviously more than other types of transposons and the Ty3/Gypsy retrotransposon proportion was greater than Ty1/Copia retrotransposons. there were no Ty1/Copia retrotransposons in Lbb CA1. Most Ty1/Copia and Ty3/Gypsy retrotransposons presented distinct evolutionary distance among different pathogen strains. Besides, the higher LTR retrotransposon density, the lower gene density, the Solo-LTR retrotransposons were much greater than intact LTR retrotransposons. Both Solo-LTR and intact LTR retrotransposon counts were the highest in Lmb V23.1.3, followed by Lbb B3.5 and Lbb CA1 respectively. Many intact LTR retrotransposons in Lmb V23.1.3 were more ancient than those in Lbb B3.5 and Lbb CA1. However, lots of homologous LTR retrotransposons in Lmb V23.1.3 were younger than those in Lbb B3.5 and Lbb CA1. No common intact LTR retrotransposons were identified between L. maculans species and L. biglobosa species, and significantly few even between two strains of the same pathogen species. Large number of special intact LTR retrotransposons in L. biglobosa were relatively younger than those in L. maculans. In addition, the LINE elements only occurred in Lmb V23.1.3, which was possibly responsible for its stronger pathogenicity. Conclusions Some pathogen strains of L. biglobosa species also contained genome transposon of distantly beyond 4%. For both L. biglobosa and L. biglobosa species, the LTR retrotransposon proportion was obviously more than other types of transposons. There was distinct evolutionary distance of LTR retrotransposons and no common intact LTR retrotransposons between two pathogen species. The Ty3/Gypsy retrotransposon proportion was greater than Ty1/Copia retrotransposons. Large number of special intact LTR retrotransposons in L. biglobosa were relatively younger than those in L. maculans. The LINE elements only occurred in Lmb V23.1.3 of L. maculans species, which was possibly responsible for its stronger pathogenicity.

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Section: Size Proportion Counts Of Various Transposons Of Blackleg Ca...mentioning

confidence: 99%

Genome transposon analysis of blackleg causal pathogen

Tian,

Hao,

et al. 2024

Preprint

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“…Among diverse types of transposons, the size, proportion and number of LTR 3, 4). The LINE transposons were found to be greatly active in human genomes (Ramos et al 2021), participating in regulation of telomere structure and leading to malignant cell proliferation and tumor formation (Mueller et al 2018).…”

Section: Size Proportion and Number Of Various Transposons Of Blackle...mentioning

confidence: 99%

Genome transposon analysis of blackleg pathogen (Leptosphaeria spp.)

Tian,

Hao,

et al. 2024

Preprint

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Background To understand presence of genome transposons of blackleg pathogen and to explore potential relationship between transposons and pathogenicity, we performed genome transposon analysis for various blackleg pathogen strains. Results The genome transposon proportion was approximately 30%, 18% and 10% in three blackleg pathogen strains, Lmb V23.1.3, Lbb B3.5 and Lbb CA1, respectively. For the three blackleg pathogen strains, the LTR retrotransposon percentage was obviously more than other types of transposons, and the counts of Ty3/Gypsy superfamily of intact LTR retrotransposons was much greater than that of Ty1/Copia superfamily. The LINE elements were only discovered in the blackleg pathogen strain Lmb V23.1.3. A great many of homologous LTR retrotransposons in Lmb V23.1.3 were younger than those in Lbb B3.5 and Lbb CA1. However, the majority of intact LTR retrotransposons in Lmb V23.1.3 were more ancient than those in Lbb B3.5 and Lbb CA1. Most of Ty1/Copia and Ty3/Gypsy superfamilies of intact LTR retrotransposons from different blackleg pathogen strains clustered into various branches in phylogeny trees. Besides, statistical analysis of gene density and LTR retrotransposon density revealed an inverse relationship between them in three blackleg pathogen strains whose solo-LTR retrotransposons were much more than intact LTR retrotransposons. The blackleg pathogen strain Lmb V23.1.3 contained the highest counts of both solo-LTR and intact LTR retrotransposons, followed by Lbb B3.5 and Lbb CA1, respectively. Pan-genome transposon analysis suggested that there no common families of intact LTR retrotransposons between L. maculans and L. biglobosa species, and fewer common families of intact LTR retrotransposons were identified even between various blackleg pathogen strains of same Leptosphaeria species. Large number of common families of intact LTR retrotransposons in L.biglobosa species were relatively younger than those in L.maculans species. Conclusions The highly virulent L.maculans species has much greater proportion of transposons compared to the weakly virulent L.biglobosa species. There was a considerable evolutionary distance among intact LTR retrotransposons from L.maculans and L.biglobosa species, and there were no common families of intact LTR retrotransposons between the two species. The genome of blackleg pathogen displayed higher proportion of LTR retrotransposons, with a relatively greater abundance of Ty3/Gypsy superfamilies of intact LTR retrotransposons compared to Ty1/Copia superfamilies. The long terminal repeats at both ends of LTR retrotransposons possibly accumulate more mutations over time, and the intermediate domains are relatively conserved. Besides, there were significantly higher number of solo-LTR retrotransposons compared to intact LTR retrotransposons, and an inverse relationship between gene density and LTR retrotransposon density was observed in the blackleg pathogen. LINE elements in Lmb V23.1.3 possibly resulted in its stronger pathogenicity in B.napus crops.

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“…For instance, promoters of LINE-1 element are found to be demethylated in cancer cells [ 54 ]. Promoter demethylation often leads to gene activation and alterations in global gene expression [ 55 , 56 ]. Conversely, methylation of TE promoters renders them inactive and is believed to be a primary mechanism for suppression of transposition in somatic cells [ 57 ].…”

Section: Transposable Element Induced Genomic/epigenomic Instability ...mentioning

confidence: 99%

Role of Transposable Elements in Genome Stability: Implications for Health and Disease

Bhat

Ghatage

Bhan

et al. 2022

IJMS

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Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.

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Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics

Cited by 10 publications

References 189 publications

Genome transposon analysis of blackleg causal pathogen

Genome transposon analysis of blackleg causal pathogen

Genome transposon analysis of blackleg pathogen (Leptosphaeria spp.)

Role of Transposable Elements in Genome Stability: Implications for Health and Disease

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