Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells
Abstract
:Simple Summary
Abstract
1. Background
2. Methods
2.1. Cell Lines and Cell Culture
2.2. qCLASH
2.3. Sequencing and Bioinformatic Analyses
2.4. Mimic Transfections
2.5. RNA Extraction
2.6. Quantitative PCR
2.7. Statistical Analysis
2.8. Western Blot
2.9. Dual Luciferase Reporter Gene Assays
3. Results
3.1. Characteristics of miRNA Hybrids Identified in Melanoma Cells
3.2. miRNA 5′ Seed-Pairing and 3′ Non-Seed Pairing (Supplementary 3′ Pairing)
3.3. Hybrid Frequency and miRNA Expression Levels
3.4. Functional Analysis of Canonical and Non-Canonical Binding Sites
3.5. miRNAs Regulating Important Pathways in Melanoma
3.6. miRNA–lncRNA Interactions
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Kozar, I.; Philippidou, D.; Margue, C.; Gay, L.A.; Renne, R.; Kreis, S. Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. Cancers 2021, 13, 1096. https://doi.org/10.3390/cancers13051096
Kozar I, Philippidou D, Margue C, Gay LA, Renne R, Kreis S. Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. Cancers. 2021; 13(5):1096. https://doi.org/10.3390/cancers13051096
Chicago/Turabian StyleKozar, Ines, Demetra Philippidou, Christiane Margue, Lauren A. Gay, Rolf Renne, and Stephanie Kreis. 2021. "Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells" Cancers 13, no. 5: 1096. https://doi.org/10.3390/cancers13051096