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| Status |
Public on Aug 17, 2020 |
| Title |
Stress-induced RNA–chromatin interactions promote endothelial dysfunction (scRNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.
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| Overall design |
Performing single-cell RNA-seq in HUVEC human cell lines in three samples: control (no treatment) and after 3 and 7 days of treatment to mimic endothelial to mesenchymal transition.
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| Contributor(s) |
Calandrelli R, Xu L, Luo Y, Wu W, Fan X, Nguyen T, Chen C, Sriram K, Natarajan R, Bouman-Chen Z, Zhong S |
| Citation(s) |
33060583, 35837599, 38251974 |
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| Submission date |
Aug 04, 2019 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Sheng Zhong |
| E-mail(s) |
szhong@eng.ucsd.edu
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| Organization name |
University of California San Diego
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| Department |
Bioengineering
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE135357 |
Stress-induced RNA–chromatin interactions promote endothelial dysfunction |
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| Relations |
| BioProject |
PRJNA558555 |
| SRA |
SRP217333 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135356_RAW.tar |
316.3 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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