Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Activations of transposon elements are associated with onset of Fragile-X disorders

ABSTRACT: We found the modifications of specific transposon elements-derived genes in FXD patients by RNA-sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE307217 | GEO | 2026/02/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Global Mapping of Transposon Location

Project description:Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome?s full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray- based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential. Keywords: transposon mapping

2006-11-15 | GSE6278 | GEO

Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity

Project description:Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity

| PRJNA1269552 | ENA

Mycoplasma pneumoniae transposon libraries

Project description:In order to study essential genomic elements in bacteria we prepare pMT85 and pMTnTetM438 mini‐transposon mutant libraries of M. pneumoniae. The dataset contains controls and the minitransposon libraries, after DNAs isolation the libraries and the controls were prepared for sequencing by HITS using standard Illumina paired‐end protocol.

2015-07-09 | E-MTAB-3075 | biostudies-arrayexpress

TE-Array-- A high throughput tool to study transposon transcription

Project description:TE-Array is a custom Agilent microarray that probes for transposable elements in both sense and antisense orientations in humans and mice. TE-Array was used to study expression levels of transposable elements (TE) in a panel of normal mouse tissues. TE-Array comprises of 4 different custom Agilent 4X44K designs. These 4 different designs have probes for human sense orientation, human antisense orientation, mouse sense orientation and mouse antisense orientation transposable elements. These array designs were used to study the transposon abundance profile in 7 different mouse tissue samples, 2 mouse cell lines and 1 transposon transfected versus untransfected human cell line.

2013-11-16 | E-GEOD-52412 | biostudies-arrayexpress

Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle

Project description:In this study, we analyzed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity, and suggest that 21 nt small RNAs play a key role in transposon silencing.Furthermore, we provide evidence that transposon-associated DNA methylation, but not sRNA production, is directly involved in the silencing of genes surrounded by transposons. Finally, we identified key genes activated in the fruiting process through the comparative analysis of transcriptomes.

2018-05-15 | GSE112588 | GEO

Transposon expression kinetics in Dnmt3L-/- developing testes [RNA-seq]

Project description:We examined the kinetics of production of mRNAs and small RNAs derived from transposable elements during mouse spermatogenesis, in whole gonads of wildtype and DNA methylation-deficient males (Dnmt3L and Miwi2 mutants). We found that in absence of DNA methylation, transposon reactivation is not constitutive but rather occurs in a class- and development-specific manner : both the intensity of reactivation and the number of reactivated transposon classes increased as germ cells progress in meiosis. Moreover, we observed that transposon silencing before meiosis is not due to increased cleavage by the piRNA machinery. In contrast, the burst of transposon transcripts occurring at meiosis in the absence of DNA methylation serve as substrates for increased piRNA production

2015-06-01 | GSE57745 | GEO

5-hydroxymethylcytosine-mediated alteration of transposon activity associated with Preeclampsia

Project description:Preeclampsia and gestational diabetes mellitus (GDM) are two of the most common clinical conditions during pregnancy that could result in adverse utero environments of the fetus. Fetal exposure to poor environments in uterus also raises the risk of future adulthood disorders known as fetal origins of adult disease (FOAD). Epigenetic modifications like cytosine methylation and histone modification have been proposed to be involved in FOAD. Recent research has implicated 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) via oxidation by ten-eleven translocation (Tet) enzymes, in DNA methylation-related plasticity. Here we show that the expression of Tet2 and 5hmC abundance significantly altered in the umbilical vessels of preeclampsia. Genome-wide profiling of 5hmC revealed differentially hydroxymethylated regions (DhMRs) associated with preeclampsia and GDM, and DhMRs were enriched among the genes involved in unique biological pathways for each condition. In particular, 5hmC significantly changed in selective transposons and led to the alteration of transposon activity in preeclampsia. The 5hmC-mediated alteration of transposon activity was further confirmed using established hypoxia cell culture model and could be rescued by Vitamin C, a known activator of Tet proteins. Together our results suggest that adverse utero environments induced by preeclampsia could influence 5hmC-mediated epigenetic profile and contribute to FOAD.

2016-05-09 | GSE75941 | GEO

Developmentally regulated piRNA clusters implicate MILI in transposon control

Project description:Nearly half of the mammalian genome is composed of repeated sequences. In Drosophila, PIWI proteins exert control over transposons. However, mammalian PIWI proteins, Miwi and Mili, partner with piRNAs that are depleted of repeat sequences, raising questions about a role for mammalian PIWIs in transposon control. A search for murine small RNAs that might program PIWI proteins for transposon suppression revealed developmentally regulated piRNA loci, some of which resemble transposon master control loci of Drosophila. We also find evidence of an adaptive amplification loop in which PIWI catalyzes formation of piRNA 5’ ends. Mili mutants de-repress L1 and IAP and lose DNA methylation of L1 elements, demonstrating an evolutionarily conserved role for PIWI proteins in transposon suppression. Keywords: small RNA profile, piRNA

2007-04-20 | GSE7414 | GEO

Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [RNA-Seq]

Project description:Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [RNA-Seq]

| PRJNA1269559 | ENA

Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [ATAC-seq]

Project description:Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity [ATAC-seq]

| PRJNA1269560 | ENA