PP2A complex disruptor SET prompts widespread hyper-transcription of growth-essential genes in the pancreatic cancer cells
Data files
Jan 23, 2024 version files 238.64 KB
-
README.md
2.63 KB
-
SET_IP-MS_in_control_and_SET-OE_cells.xlsx
236.01 KB
Abstract
Hyper-activation of the oncogenic transcription reflects the epigenetic plasticity of the cancer cells. SET was described as a nuclear factor that stimulated transcription from the chromatin template. However, the mechanisms of SET-dependent transcription are unknown. Here, we found that over-expression of SET and CDK9 induced very similar transcriptome signatures in multiple cancer cell lines. SET localized in the transcription start site (TSS)-proximal regions and supported the RNA transcription. SET specifically bound the PP2A-C subunit and induced PP2A-A subunit repulsion from the C subunit, which indicated the role of SET as a PP2A-A/C complex disruptor in the TSS-proximal regions. Through blocking PP2A activity, SET assisted CDK9 to maintain Pol II CTD phosphorylation and activated mRNA transcription. Our findings position SET as a key factor that modulates chromatin PP2A activity, promoting the oncogenic transcription in pancreatic cancer.
README: PP2A complex disruptor SET prompts widespread hyper-transcription of growth-essential genes in the pancreatic cancer cells
https://doi.org/10.5061/dryad.9p8cz8wpr
Usage notes
This dataset contains the results of the SET protein complex analysis. It also provides the way to access other supplementary data of this research.
Datasets included:
1) SET protein complex analysis in the HEK293T cells
- 10 million HEK293T cells were stably transfected with the control and Myc-SET plasmids, respectively.
- Magnetic beads conjugated with anti-SET antibody were added to the control and SET-OE cell lyastes.
- The control SET and SET-OE associated proteins were immunoprecipitated with magnetic beads and subjected to SDS-PAGE separation.
- Thermo UltiMate 3000 UHPLC was utilized to separate samples of dried peptides. The liquid phase chromatography-separated peptides were ionized by a nanoESI source and passed to a tandem mass spectrometer Q-Exactive HF X for Data Dependent Acquisition mode detection.
- For each detectable peptide of the SET associated proteins in the control and SET-OE cells, the iBAQ value was calculated and shown with the Protein ID in the datasheet (see the worksheet named "HEK293T" in the appended Excel file).
2) SET protein complex analysis in the Panc02 cells
- 10 million Panc02 cells were stably transfected with the control and SET overexpressing lentivirus, respectively.
- Magnetic beads conjugated with anti-SET antibody were added to the control and SET-OE cell lyastes.
- The control SET and SET-OE associated proteins were immunoprecipitated with magnetic beads and subjected to SDS-PAGE separation.
- Thermo UltiMate 3000 UHPLC was utilized to separate samples of dried peptides. The liquid phase chromatography-separated peptides were ionized by a nanoESI source and passed to a tandem mass spectrometer Q-Exactive HF X for Data Dependent Acquisition mode detection.
- For each detectable peptide of the SET associated proteins in the control and SET-OE cells, the iBAQ value was calculated and shown with the Protein ID in the datasheet (see the worksheet named "Panc02" in the appended Excel file).
3) The other high-throughput sequencing results associated with the research.
Sharing/Access information
Alternatively, we have deposited the supplementary data including this IP-MS results, nascent RNA-seq, RNA-seq, ChIP-seq and CUT&Tag data reported in this paper to Mendeley Data (https://data.mendeley.com/datasets/ys5kswxvw7/draft?a=3f82e213-d935-4e74-b88c-f5968b9417a1).
Code/Software
No new code or software in this research.