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| Status |
Public on Jan 10, 2022 |
| Title |
The homeotherm-conserved protein CGGBP1 connects heat stress to chromosomal fusions |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
Methylation profiling by high throughput sequencing
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| Summary |
We report that heat stress induces chromosomal fusion events in cell culture. We describe the findings first using normal primary fibroblasts [Coriell Cell Repository GM02639] and subsequently apply it to a system of HEK293T stable lines called CT and KD [described in PMID 31547883]. The stable line CT stands for Control shRNA and KD stands for a knockdown of human CGGBP1 using specific shRNA [Origene Lentiviral system TL313955V]. Our results suggest that as measured by the frequency of chromosomal fusions, the CGGBP1 knockdown in KD, when compared to CT, imitates the effects of heat stress. Further, ChIP-sequencing for TP53BP1 show genome-wide misdirected repairs at repeat flanks in KD as compared to CT. We show that CGGBP1 depletion and heat give rise to chromosomal fusions due to overlapping mechanisms that involve misdirected repair in the flanks of repeats genome-wide.
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| Overall design |
Genomic DNA was isolated and MeDIP-seq was perforrmed for GM01391-CT and -KD as described elsewhere (PMID: 32727353 and GSE145300) on IonTorrent platform. For genotype identification, parental DNA from fibroblasts (GM01392 and GM01393 from Coriell Repository) were also sequenced on the same platform. The analysis parameters for read QC, alignment, variant calling were as described in PMID: 32727353.
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| Contributor(s) |
Singh U, Datta S, Patel M, Patel D, Kashyap S |
| Citation(s) |
35070079 |
| |
| Submission date |
Mar 23, 2021 |
| Last update date |
Apr 11, 2022 |
| Contact name |
Umashankar Singh |
| Organization name |
IIT Gandhinagar
|
| Department |
Biological Sciences and Engineering
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| Lab |
HoMeCell Lab
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| Street address |
Acad Block 4 Room 317 IIT Gandhinagar Palaj
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| City |
Gandhinagar |
| State/province |
Gujarat |
| ZIP/Postal code |
382055 |
| Country |
India |
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| Platforms (2) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA716602 |
| SRA |
SRP311816 |
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