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

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

PROVIDER: PRJNA507092 | ENA |

REPOSITORIES: ENA

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Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Capture 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 | GSE122975 | GEO

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

2018-11-28 | GSE122976 | GEO

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 (4C-Seq)

2018-11-28 | GSE122974 | GEO

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

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

| PRJNA507088 | ENA

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 genomic interactions identifies candidate host genes that transposable elements potentially regulate.

Project description: Not available

| S-EPMC6292174 | biostudies-literature

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

Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

Project description:Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

| PRJNA755723 | ENA

Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

Project description:Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of Hi-ChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we show that young TEs display locus- and tissue-specific chromatin profiles in both mice and humans. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

2021-08-19 | GSE182305 | GEO

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