Transposable Elements

Guffanti, Guia; Bartlett, Andrew A.; DeCrescenzo, Paula; Macciardi, Fabìo; Hunter, Richard G.

doi:10.1007/7854_2019_112

Cited by 13 publications

(6 citation statements)

References 144 publications

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“…Stress is an ubiquitous environmental stimuli that is both perceived and adapted to by the brain. Stress has certainly been associated with pathogenesis of numerous neuropsychiatric disorders including anxiety, depression, and post-traumatic stress disorder ( Bartlett et al, 2017 ; Guffanti et al, 2019 ). Physiologically, stress stimuli produce a signaling cascade through hypothalamic-pituitary-adrenal axis activation, resulting in the release of glucocorticoids which can diffuse and subsequently act on receptors within the brain including the hippocampus.…”

Section: Introductionmentioning

confidence: 99%

Corticosterone dynamically regulates retrotransposable element expression in the rat hippocampus and C6 cells

Bartlett

DeRosa

Clark

et al. 2021

Neurobiology of Stress

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The hippocampus is a highly plastic brain region sensitive to environmental stress. It shows dynamic changes in epigenetic marks associated with stress related learning. Previous work has shown that acute stress induces substantial transient changes in histone H3 lysine 9 trimethylation (H3K9me3). Moreover, increased H3K9me3 is enriched in hippocampal gene deserts accumulating within endogenous retroviruses and transposable elements. We have found that in response to acute glucocorticoid treatment, a similar change in global H3K9me3 is observed. However, when localized we found that H3K9me3 is markedly decreased at B2 short interspersed nuclear elements but not within intracisternal-A particle endogenous retroviruses. Further, decreased H3K9me3 valence within B2 elements was associated with increased transcript abundance. These data demonstrate the capacity for acute glucocorticoids to mobilize transposable elements via epigenetic unmasking. Reconciled with previous findings following acute stress, this suggests the capacity for mobile elements to potentially function as novel regulators given their dynamic regulation by stress and glucocorticoids.

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Section: Introductionmentioning

confidence: 99%

Corticosterone dynamically regulates retrotransposable element expression in the rat hippocampus and C6 cells

Bartlett

DeRosa

Clark

et al. 2021

Neurobiology of Stress

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“…The overall frequency of nucleotide substitutions and indels increased in the TEs-excised site [ 44 ]. TEs activation can trigger the generation of tandem repeats [ 45 ], and the genomic structure can be modified by the insertion of MITEs without TPase. Gene expression may be affected by the activation or inactivation of MITEs or by small RNA derived from MITEs [ 46 , 47 ].…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of PTE-2, a Stowaway-like MITE Activated in Transgenic Chinese Cabbage Lines

Jeon

Shin

Cheon

et al. 2022

Genes

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Transposable elements (TEs) are DNA fragments that can be replicated or transposed within a genome. TEs make up a high proportion of the plant genome and contribute to genetic diversity and evolution, affecting genome structure or gene activity. Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II DNA transposable elements. MITEs have specific sequences, target site duplications(TSDs), and terminal inverted repeats(TIRs), which are characteristics of the classification of MITE families. In this study, a Stowaway-like MITE, PTE-2, was activated in transgenic Chinese cabbage lines. PTE-2 was revealed by in silico analysis as the putative activated element in transgenic Chinese cabbage lines. To verify the in silico analysis data, MITE insertion polymorphism (MIP) PCR was conducted and PTE-2 was confirmed to be activated in transgenic Chinese cabbage lines. The activation tendency of the copy elements of PTE-2 at different loci was also analyzed and only one more element was activated in the transgenic Chinese cabbage lines. Analyzing the sequence of MIP PCR products, the TSD sequence and TIR motif of PTE-2 were identified and matched to the characteristics of the Stowaway-like MITE family. In addition, the flanking region of PTE-2 was modified when PTE-2 was activated.

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“…TEs make up to two-thirds of the human genome and are known to play important roles in molecular functions [ 21 ]. TEs such as LINEs and SINEs have numerous effects on the genome, including genomic rearrangements and the regulation of gene [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

DNA Hypermethylation and a Specific Methylation Spectrum on the X Chromosome in Turner Syndrome as Determined by Nanopore Sequencing

Fan

Zhang

Fan

et al. 2022

JPM

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The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 × 10−16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS.

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Transposable Elements

Cited by 13 publications

References 144 publications

Corticosterone dynamically regulates retrotransposable element expression in the rat hippocampus and C6 cells

Corticosterone dynamically regulates retrotransposable element expression in the rat hippocampus and C6 cells

Identification and Characterization of PTE-2, a Stowaway-like MITE Activated in Transgenic Chinese Cabbage Lines

DNA Hypermethylation and a Specific Methylation Spectrum on the X Chromosome in Turner Syndrome as Determined by Nanopore Sequencing

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