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| Status |
Public on Sep 30, 2020 |
| Title |
Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
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| Overall design |
The genome-wide interactome were generated using in-situ Hi-C method in both ltwo-dimensional (2D) and three-dimensional (3D) cultured AML12 cells which were arrest at G1/S
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| Contributor(s) |
Liu X, Sun Q, Shao Z |
| Citation(s) |
33631432 |
| Submission date |
Aug 22, 2019 |
| Last update date |
Feb 28, 2021 |
| Contact name |
Xin Liu |
| E-mail(s) |
xinliu@sjtu.edu.cn
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| Organization name |
Shanghai Jiaotong University
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| Department |
School of Biomedical Engineering
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| Street address |
800 Dong Chuan Rd.
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platforms (1) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE136307 |
Epithelial cells in 2D and 3D culture exhibit significant differences in long-range genomic interactions |
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| Relations |
| BioProject |
PRJNA561501 |
| SRA |
SRP219431 |
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