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| Status |
Public on Nov 06, 2019 |
| Title |
Involvement of Condensin in Cellular Senescence through Gene Regulation and Compartmental Reorganization |
| Organism |
Homo sapiens |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Cellular senescence is a state of stable cell growth arrest induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively. Senescence is accompanied not only by global transcriptional alterations but also by 3D genome reorganization. Here we demonstrate that the human condensin II complex participates in cellular senescence via gene regulation and reorganization of euchromatic A and heterochromatic B chromatin compartments. OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and account for 15% of the human genome. Mechanistically, condensin is enriched at A compartments, especially at gene promoters and typical/super enhancers, and implicated in the B-to-A transitions. Genes present at B-to-A-switching regions tend to be up-regulated. The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers such as the activity of senescence-associated beta-galactosidase (SA-beta-gal) and senescence-associated heterochromatic foci (SAHF). This study describes that condensin reinforces euchromatic A compartments and is required for optimal expression of senescence genes, thereby contributing to the establishment and maintenance of the senescent state.
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| Overall design |
in situ HI-C with human senescence cells. ChIP-seq and RNA-seq with human senescence cells. Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 x MEM non-essential amino acids. Growing cells in population doublings (PD) between 26 and 32 were used for experiments. pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging. H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. For CAP-H2 knockdown, pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon: CAPH2_KD1, 2, 3) and empty vector (control) were used. Doxycycline (1ug/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression. OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (KD1, 2, and 3) against NCAPH2 and harvested 3 days after the lentivirus infection.
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| Contributor(s) |
Tanizawa H, Noma K |
| Citation(s) |
31831736 |
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| Submission date |
Aug 13, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
hidekit@uoregon.edu
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| Organization name |
University of Oregon
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| Department |
Institute of Molecular Biology
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| Street address |
1370 Franklin Blvd
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| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (50)
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| Relations |
| BioProject |
PRJNA485804 |
| SRA |
SRP157799 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE118494_RAW.tar |
7.7 Gb |
(http)(custom) |
TAR (of BW, TAR, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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