Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Capture of a functionally active Methyl-CpG Binding Domain by an arthropod retrotransposon family

ABSTRACT: The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Unexpectedly, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD domain. We functionally demonstrate how retrotransposon encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host genome, in the myriapod Strigamia maritima. Consistently, young MBD-encoding Copia retrotransposons (CopiaMBD) accumulate in regions with higher CpG-densities than other LTR-retrotransposons also present in the genome. This would suggest that retrotransposons use MBDs to integrate into heterochromatic regions in Strigamia, avoiding potentially harmful insertions into host genes. In contrast, CopiaMBD insertions in the spider Stegodyphus dumicola genome disproportionately accumulate in methylated gene bodies when compared to other spider LTR-retrotransposons. Given that transposons are not actively targeted by DNA methylation in the spider genome, this distribution bias would also support a role for MBDs in the integration process. Together, these data demonstrate that retrotransposons can co-opt host-derived epigenome readers, potentially harnessing the host epigenome landscape to advantageously tune the retrotransposition process.

ORGANISM(S): Strigamia maritima

PROVIDER: GSE118012 | GEO | 2019/06/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [RNA-Seq]

Project description:Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of Methyl-CpG Binding Domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse stem cells, derived neurons or a human cell line does not reactivate genes or repeats with methylated promoters. These do however become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation-sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.

2022-09-29 | GSE184469 | GEO

Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [ATAC-Seq]

2022-09-29 | GSE184467 | GEO

Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [WGBS-Seq]

2022-09-29 | GSE207255 | GEO

Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [ChIP-Seq]

2022-09-29 | GSE184468 | GEO

Arrested replication forks guide retrotransposon integration

Project description:Long Terminal Repeat (LTR) Retrotransposons are an abundant class of genomic parasites that replicate by insertion of new copies into the host genome. LTR retrotransposons prevent mutagenic insertions through diverse targeting mechanisms that avoid coding sequences, but a universal set of principles guiding their target site selection hasn’t been established. Here we show that insertion of the fission yeast LTR retrotransposon Tf1 is guided by the DNA binding protein Sap1, and that the efficiency and location of the targeting depend on the activity of Sap1 as a replication fork barrier. We propose that Sap1 guides insertion of Tf1 by blocking the progression of the replication fork, and that the Tf1 transposon uses features of arrested forks to insert into the host genome. These observations point to a universal mechanism for determination of LTR retrotransposon target site selection.

2015-09-25 | GSE67692 | GEO

OsJMJ703, a Histone H3K4 Demethylase, Controls Transposon Activity in Rice

Project description:Retrotransposons are classified into long terminal repeat (LTR) or non-LTR retrotransoposons, and both types can mobilize in a “copy and paste” manner. Rice genome contains >40% of repetitive sequences or transposable elements (TEs) that scattered throughout the genome. TE activities are tightly regulated by distinct epigenetic mechanisms. Histone lysine methylation is catalyzed by SET domain group (SDG) protein and reversed by a family of Jumonji C (JmjC) domain-containing proteins. In rice, DNA methylation and histone methylation have been implicated in controlling copia-like LTR retrotransposon Tos17 activities. Whether any TEs are controlled by histone demethylase remains to be elusive. Here, we show that JMJ703 is a histone H3K4 specific demethylase in rice. Impaired JMJ703 disrupted genome-wide transcriptome and enhanced H3K4me3 resulting in pleiotropic defects. Two LINE elements, Karma and its N-terminal truncation were identified as direct targets of JMJ703 with increased frequency of transposition in jmj703, while Tos17 is unaffected. Our findings show that plants use H3K4me3 demethylase to constitutively remove active chromatin mark and maintain silencing status at a subset retrotransposons which localize in heterochromatin regions. Therefore, our work uncovers a novel mechanism to control retrotransposon activity by histone demethylation, which further strengthens the link between epigenetic silencing and genome stability. Examination of differences in H3K4 between jmj703 and wild type.

2013-01-01 | E-GEOD-41183 | biostudies-arrayexpress

Centrophilic retrotransposon integration via targeting CENH3 chromatin in Arabidopsis [ChIP-Seq]

Project description:In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.

2024-08-08 | GSE263225 | GEO

Centrophilic retrotransposon integration via targeting CENH3 chromatin in Arabidopsis [TED-seq]

2024-08-08 | GSE263224 | GEO

The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [RNA-seq]

Project description:Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

2023-01-06 | GSE196869 | GEO

The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [ALE-seq]

2023-01-06 | GSE196868 | GEO