YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Abstract
1. Introduction
2. Results
2.1. YBX1 Is an Essential RBP for Cell Survival in Medulloblastomas
2.2. YBX1 Controls Inflammatory Response and Apoptosis Genes
2.3. YBX1 Targets 3′UTRs and Indirectly Regulates Heterochromatin-Repressed Apoptosis-Related Inflammatory Response Genes
3. Discussion
4. Materials and Methods
4.1. Cell Lines
4.2. qRT-PCR
4.3. Western Blot and Protein Localization
4.4. siRNA-Mediated Knockdown
4.5. Cell Viability Assay
4.6. RNA-Seq
4.7. PAR-CLIP
4.8. Bioinformatics
4.8.1. RNA-Seq
4.8.2. Pathway Analysis
4.8.3. PAR-CLIP
4.8.4. ChIP-Seq Data Integration
Author Contributions
Funding
Conflicts of Interest
Abbreviations
CBX5 | Chromobox protein homolog 5 |
FDR | False discovery rate |
H3K9me3 | Histone 3 K9 tri-methylation |
IPA | Ingenuity pathway analysis |
KD | Knockdown |
PAR-CLIP | Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation |
PBS | Phosphate buffered saline |
RBP | RNA binding protein |
RNA-seq | RNA sequencing |
ChIP-seq | Chromatin-immunoprecipitation and sequencing |
Ssh | Sonic hedgehog signaling |
Wnt | Wnt signaling |
YBX1 | Y-box binding protein 1 |
Appendix A
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Kloetgen, A.; Duggimpudi, S.; Schuschel, K.; Hezaveh, K.; Picard, D.; Schaal, H.; Remke, M.; Klusmann, J.-H.; Borkhardt, A.; McHardy, A.C.; et al. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. Int. J. Mol. Sci. 2020, 21, 4453. https://doi.org/10.3390/ijms21124453
Kloetgen A, Duggimpudi S, Schuschel K, Hezaveh K, Picard D, Schaal H, Remke M, Klusmann J-H, Borkhardt A, McHardy AC, et al. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. International Journal of Molecular Sciences. 2020; 21(12):4453. https://doi.org/10.3390/ijms21124453
Chicago/Turabian StyleKloetgen, Andreas, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan-Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, and et al. 2020. "YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA" International Journal of Molecular Sciences 21, no. 12: 4453. https://doi.org/10.3390/ijms21124453
APA StyleKloetgen, A., Duggimpudi, S., Schuschel, K., Hezaveh, K., Picard, D., Schaal, H., Remke, M., Klusmann, J.-H., Borkhardt, A., McHardy, A. C., & Hoell, J. I. (2020). YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. International Journal of Molecular Sciences, 21(12), 4453. https://doi.org/10.3390/ijms21124453