Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. ChIP-Seq Data
2.1.1. Downloading ChIP-Seq Datasets
2.1.2. Quantification of ChIP-Seq Signals Using Easeq
2.1.3. Data Analysis
Heat Maps
Line Tracks
Binding Overlap Analysis
Source | Cell Type | ChIP-Seq File Type | Accession |
---|---|---|---|
Sanidas et al., 2022 [101] | BJ cells | FLAG-RB-WT | SRR14713166 |
FLAG-RB-Δcdk | SRR14713167 | ||
RPE cells | FLAG-RB-WT Input | SRR14713168 | |
FLAG-RB-Δcdk Input | SRR14713169 | ||
FLAG-RB-WT | SRR14713063 | ||
FLAG-RB-Δcdk | SRR14713064 | ||
FLAG-RB-WT Input | SRR14713079 | ||
FLAG-RB-Δcdk Input | SRR14713080 | ||
E2F1 | SRR14713081 | ||
Michael Snyder, Stanford. 2017 | K562 cells | RB1 | ENCFF305NFS |
Richard Myers, HAIB. 2023 | E2F1 | ENCFF183WQN | |
ENCFF193ODF | |||
E2F4 | ENCFF706ZTX | ||
ENCFF749XCO | |||
E2F5 | ENCFF027ECD | ||
ENCFF915WXK | |||
Chicas et al., 2010 [102] | Growing IMR90 cells | RB | SRR034478 |
SRR034479 | |||
Mock | SRR034492 | ||
Quiescent IMR90 cells | RB | SRR034480 | |
SRR034482 | |||
Mock | SRR034493 | ||
Senescent IMR90 cells | RB | SRR034484 | |
SRR034486 | |||
Mock | SRR034494 | ||
Quiescent IMR90 cells | p130 | SRR034483 | |
Ferrari et al., 2012 [103] | Quiescent IMR90 cells | p107 | SRR350272 |
2.2. ChIP-Atlas Data
3. Results
3.1. RB and p130 Associate with Many tRNA Genes in Human Fibroblasts
3.2. Phosphoresistant Mutation Stimulates Binding of RB to tRNA Genes
3.3. RB Recruitment to Many tRNA Genes Coincides with Binding Sites for E2F
3.4. RB May Be Recruited by E2F to 7SL and RMRP Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sizer, R.E.; Butterfield, S.P.; Hancocks, L.A.; Gato De Sousa, L.; White, R.J. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers 2024, 16, 481. https://doi.org/10.3390/cancers16030481
Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers. 2024; 16(3):481. https://doi.org/10.3390/cancers16030481
Chicago/Turabian StyleSizer, Rebecca E., Sienna P. Butterfield, Lucy A. Hancocks, Leonor Gato De Sousa, and Robert J. White. 2024. "Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III" Cancers 16, no. 3: 481. https://doi.org/10.3390/cancers16030481