All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing

Stefano, Luisa Di

doi:10.3390/cells11162501

Cited by 4 publications

(2 citation statements)

References 219 publications

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“…Finally, TEs can disrupt normal gene regulatory networks by influencing the expression of nearby genes through their regulatory sequences 7 . Due to their pathogenic potential, TEs are kept under tight control by the host with multiple regulatory layers 8 . DNA methylation is one of the main ways by which cells silence TEs 9 .…”

Section: Introductionmentioning

confidence: 99%

Transposable element methylation state predicts age and disease

Morandini,

Lu,

Rechsteiner

et al. 2024

Preprint

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Transposable elements (TEs) are DNA sequences that expand selfishly in the genome, possibly causing severe cellular damage. While normally silenced, TEs have been shown to activate during aging. DNA methylation is one of the main mechanisms by which TEs are silenced and has been used to train highly accurate age predictors. Yet, one common criticism of such predictors is that they lack interpretability. In this study, we investigate the changes in TE methylation that occur during human aging. We find that evolutionarily young LINE1s (L1s), the only known TEs capable of autonomous transposition in humans, undergo the fastest loss of methylation, suggesting an active mechanism of de-repression. We then show that accurate age predictors can be trained on both methylation of individual TE copies and average methylation of TE families genome wide. Lastly, we show that while old L1s gradually lose methylation during the entire lifespan, demethylation of young L1s only happens late in life and is associated with cancer.

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Section: Introductionmentioning

confidence: 99%

Transposable element methylation state predicts age and disease

Morandini,

Lu,

Rechsteiner

et al. 2024

Preprint

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“…Organisms living in challenging environmental conditions can have more TEs in their genome, increasing genome plasticity to respond to stress factors [ 33 ]. TEs can be divided into two classes based on their replication mechanisms: Class I elements transpose with RNA-mediated mechanisms (retrotransposons), while in Class II the transposition mode is DNA-based (DNA transposons) [ 34 , 35 , 36 , 37 ]. In Class I, LTR retrotransposons and Penelope-like elements are characterized by Long Terminal Repeat (LTR).…”

Section: Introductionmentioning

confidence: 99%

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

Rutz

Bonassin

Francesconi

et al. 2023

Genes

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Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

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The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders

Frost,

Dubnau

2024

Annual Review of Neuroscience

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Over 40% of the human genome is composed of retrotransposons, DNA species that hold the potential to replicate via an RNA intermediate and are evolutionarily related to retroviruses. Retrotransposons are most studied for their ability to jump within a genome, which can cause DNA damage and novel insertional mutations. Retrotransposon-encoded products, including viral-like proteins, double-stranded RNAs, and extrachromosomal cytoplasmic DNAs, can also be potent activators of the innate immune system. A growing body of evidence suggests that retrotransposons are activated in age-related neurodegenerative disorders and that such activation causally contributes to neurotoxicity. Here we provide an overview of retrotransposon biology and outline evidence of retrotransposon activation in age-related neurodegenerative disorders, with an emphasis on those involving TAR-DNA binding protein-43 (TDP-43) and tau. Studies to date provide the basis for ongoing clinical trials and hold promise for innovative strategies to ameliorate the adverse effects of retrotransposon dysregulation in neurodegenerative disorders.

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All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing

Cited by 4 publications

References 219 publications

Transposable element methylation state predicts age and disease

Transposable element methylation state predicts age and disease

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders

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