Taming transposable elements in vertebrates: from epigenetic silencing to domestication

Almeida, Miguel Vasconcelos; Vernaz, Grégoire; Putman, Audrey L K; Miska, Eric A.

doi:10.1016/j.tig.2022.02.009

Cited by 90 publications

(103 citation statements)

References 298 publications

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“…There are at least two pathways of H3K9me3-mediated TE silencing in human cells: by the KZNF/KAP1 system (described in the next section), or by the human silencing hub (HUSH) complex partnering with the ATPase MORC2. HUSH preferentially binds young, full-length L1s within euchromatic regions, indicating that this is a targeted mechanism of host defense with the capacity to respond to novel insertions [ 132 ]. Another important histone modification involved in (less stringent) TE silencing is H3K27 tri-methylation (H3K27me3) deposited by the Polycomb repressive complex 2 (PRC2).…”

Section: Mobile Genetic Elements In the Human Genome And Their Regula...mentioning

confidence: 99%

The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology

Чеснокова

Beletskiy

Kolosov

2022

IJMS

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Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.

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Section: Mobile Genetic Elements In the Human Genome And Their Regula...mentioning

confidence: 99%

The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology

Чеснокова

Beletskiy

Kolosov

2022

IJMS

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“…When inserted into noncoding DNA, including introns, they can affect the host gene expression in cis or trans . Most TEs are incapable of transposing due to acquired mutations, epigenetic, and post-transcriptional silencing mechanisms, reviewed in (Almeida et al, 2022; Molaro and Malik, 2016). However, TEs are transiently upregulated during the early development (Jachowicz et al, 2017), in the neuronal lineage (Upton et al, 2015) and cancer (Hancks and Kazazian, 2016).…”

Section: Introductionmentioning

confidence: 99%

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function

Pal

Patel

Boulet

et al. 2022

Preprint

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Mammalian genomes harbor a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition. Although most TEs are epigenetically repressed, transcriptional silencing is partially released to permit developmental or tissue-specific expression of TEs. Some TEs have also evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded transcription factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Previously, the noncoding long terminal repeat (LTR) part of the endogenous retrovirus (ERV) families has been shown to function as enhancers. We show that new LTR families and the promoter region of LINE1 (L1) are enriched with H4K16ac and H3K122ac and the chromatin features associated with active enhancers. Depletion of MSL complex and H4K16ac levels leads to a significant reduction in the expression of L1 and ERV/LTRs. We demonstrate that H4K16ac regulates TE transcription by maintaining a permissive chromatin structure. Furthermore, CRISPR-based perturbation of candidate TEs led to the downregulation of genes in cis. We conclude that H4K16ac and H3K122ac regulate a significant portion of the mammalian genome by opening local chromatin structure and transcriptional activity at TEs.

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“… A summary illustrating how transposable elements regulate sexual development. Figures were adapted from various sources ( McCarthy, 2020 ; Hermant and Torres-Padilla, 2021 ; Senft and Macfarlan, 2021 ; Almeida et al, 2022 ; Fueyo et al, 2022 ). Created with BioRender.com by Stephen Renjie Hu.…”

Section: Transposable Elementsmentioning

confidence: 99%

“…Further, ancestral state construction suggested that TEs propagated the transition to eusociality ( Chak et al, 2021 ). How and when TEs became domesticated and beneficial for the host has been discussed ( Almeida et al, 2022 ), but this is beyond the scope of this review. The evolutionary routes by which TEs became domesticated, and which types of TEs are more prone to be domesticated are still unknown.…”

Section: Systematic Functions Of Transposable Elementsmentioning

confidence: 99%

The Role of Transposable Elements in Sexual Development

Chiang

DeRosa

Park

et al. 2022

Front. Behav. Neurosci.

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Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.

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Taming transposable elements in vertebrates: from epigenetic silencing to domestication

Cited by 90 publications

References 298 publications

The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology

The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function

The Role of Transposable Elements in Sexual Development

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