The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. apoERα Activity Regulates the Expression of RBPs and SFs in the MCF-7 BC Cell Line
2.2. EMT-Related Gene Isoforms Are Differentially Expressed upon apoERα Silencing
2.3. apoERα Depletion Induces Internal ASEs in EMT-Related Genes
2.4. The apoERα-Regulated RBPs Are Significantly Correlated with ERα mRNA Levels in ERα+ BCs and Are Predicted Regulators of the apoERα-Modulated ASEs
2.5. apoERα-Regulated Exons Are Differentially Included in Primary BCs and Correlate with ERα mRNA Levels
3. Discussion
4. Materials and Methods
4.1. RNA-Seq Read Preprocessing, Alignment, and Expression Quantification
4.2. The Differential Expression Analysis
4.3. The Gene Ontology Enrichment Analysis
4.4. The Isoform Switching Analysis
4.5. The Differential Alternative Splicing Analysis
4.6. The RBP Binding Motif Enrichment Analysis
4.7. An Overlap with Alternative Splicing Events in Primary Tumor Data
4.8. The Correlation Analysis between ERα mRNA Levels and RNA-Binding Proteins Encoding Genes in ERα+ Breast Tumor Samples
4.9. The Overlap with ERα HITS-CLIP Data
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Elhasnaoui, J.; Ferrero, G.; Miano, V.; Cutrupi, S.; De Bortoli, M. The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers 2021, 13, 6261. https://doi.org/10.3390/cancers13246261
Elhasnaoui J, Ferrero G, Miano V, Cutrupi S, De Bortoli M. The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. Cancers. 2021; 13(24):6261. https://doi.org/10.3390/cancers13246261
Chicago/Turabian StyleElhasnaoui, Jamal, Giulio Ferrero, Valentina Miano, Santina Cutrupi, and Michele De Bortoli. 2021. "The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells" Cancers 13, no. 24: 6261. https://doi.org/10.3390/cancers13246261