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| Status |
Public on Apr 02, 2024 |
| Title |
3D genomics analysis identifies enhancer hijacking caused by structural alterations and extrachromosomal circular DNA formation [HiChIP] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Enhancer hijacking, caused by structural alterations, is a common cancer driver event that causes aberrant expression of oncogenes. Unfortunately, enhancer hijacking is difficult to detect due to the complexity of the cancer genome. Here we propose a simple yet robust strategy HAPI (Highly Active Promoter Interactions) to identify and characterize such events by following two rules: 1) oncogenes subject to enhancer hijacking should be potentially highly regulated by enhancers, 2) the hijacked enhancers should contribute an appreciable proportion of an oncogene’s overall enhancer activity. Applying this strategy to HiChIP data we and others generated in 34 cancer cell lines, we identified known enhancer hijacking events and uncovered novel enhancers hijacked by known or potentially novel oncogenes such as CCND1, ETV1, ID4, and NKX2-5, which we validated using CRISPRi assays and RNA-seq analysis. Furthermore, we found that complex enhancer hijacking events connecting genes and enhancers from multiple chromosomal segments are often caused by the formation of extrachromosomal circular DNA (ecDNA). Focusing on ecDNAs harboring the MYC oncogene, one of the most common gene targets of ecDNA, we found that these ecDNAs often stitch additional genes such as CDX2, ERBB2, and NFIB from other chromosomes to the MYC locus. These genes heavily hijack MYC enhancers for their activation, a novel insight into ecDNA biology, suggesting alternative therapeutic targets for MYC ecDNAs. Our study provides an efficient strategy to detect enhancer hijacking events, and more importantly reveals novel mechanisms underlying oncogene activation caused by simple or complex structural alterations.
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| Overall design |
H3K27ac HiChIP assays were performed to map enhancer-promoter interactions in cell lines of different cancer types
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| Contributor(s) |
Mortenson KL, Zhang X, Varley KE |
| Citation missing |
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| |
| Submission date |
Mar 27, 2023 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Xiaoyang Zhang |
| E-mail(s) |
xiaoyang.zhang@hci.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Oncological Sciences
|
| Lab |
Zhang
|
| Street address |
1950 Circle of Hope Drive
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE228247 |
3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression |
|
| Relations |
| BioProject |
PRJNA949128 |
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