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Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate

ABSTRACT: Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate

PROVIDER: PRJNA507088 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8246580.fastq.gz	Fastqsanger.gz
	SRR8246590.fastq.gz	Fastqsanger.gz
	SRR8246600_1.fastq.gz	Fastqsanger.gz
	SRR8246600_2.fastq.gz	Fastqsanger.gz
	SRR8246581.fastq.gz	Fastqsanger.gz

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Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (4C-Seq)

Project description:Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (4C-Seq)

| PRJNA507091 | ENA

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Hi-C)

Project description:Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Hi-C)

| PRJNA507094 | ENA

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Capture Hi-C)

Project description:Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Capture Hi-C)

| PRJNA507092 | ENA

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Hi-C)

Project description:The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation. Using adapted PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. 4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control.

2018-11-28 | GSE122976 | GEO

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (4C-Seq)

2018-11-28 | GSE122974 | GEO

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Capture Hi-C)

2018-11-28 | GSE122975 | GEO

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Project description:Transposable elements (TEs) are major contributors of genetic material in mammalian genomes. These often include binding sites for architectural proteins, including the multifarious master protein, CTCF, which shapes the 3D genome by creating loops, domains, compartment borders and RNA-DNA interactions, all of which play a role in the compact packaging of DNA and have the potential to facilitate regulatory function. In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. We show that specific (sub-)families of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species. In many cases, these loops may facilitate interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner. An experimental validation of our analytical findings using CRISPR-Cas9 to delete a candidate TE resulted in disruption of species-specific 3D chromatin structure. Taken together, we comprehensively quantify and selectively validate our finding that TEs contribute to 3D genome organization and may, in some cases, impact gene regulation during the course of mammalian evolution.

2023-01-16 | GSE222526 | GEO

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate.

Project description:BackgroundThe organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. Thus, it is challenging to identify the activities and properties of individual transposons. As a result, we only have a partial understanding of how transposons contribute to chromatin folding and how they impact gene regulation.ResultsUsing PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. With 4Tran-PCR, reads are selectively mapped to unique regions in the genome. This enables the identification of transposable element interaction profiles for individual ERV families and integration events specific to particular genomes. With this approach, we demonstrate that transposons engage in long-range intra-chromosomal interactions guided by the separation of chromosomes into A and B compartments as well as topologically associated domains (TADs). In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes.Conclusions4Tran provides new insight into the manner in which transposons contribute to chromosome architecture and identifies target genes that transposable elements can potentially control.

| S-EPMC6292174 | biostudies-literature

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

Project description:Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

| PRJNA922468 | ENA

Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-11-28 | GSE122977 | GEO