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| Status |
Public on Nov 28, 2018 |
| Title |
Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate (Hi-C) |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
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.
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| Overall design |
We used the Hi-C protocol to identify chromosomal interactions from HeLa cells treated with interferon gamma.
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| Contributor(s) |
Skok JA |
| Citation(s) |
30541598 |
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| Submission date |
Nov 27, 2018 |
| Last update date |
May 10, 2019 |
| Contact name |
Ramya Raviram |
| E-mail(s) |
rraviram@ucsd.edu
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| Organization name |
University of California San Diego
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| Lab |
Ren lab
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE122977 |
Analysis of 3D interactions identifies candidate host genes that transposable elements potentially regulate |
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| Relations |
| BioProject |
PRJNA507094 |
| SRA |
SRP170855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122976_RAW.tar |
150.8 Mb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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