Alfert, Amelie ; Walter, Carolin ; Moreno, Natalia ; Melcher, Viktoria; Graf, Monika ; Hotfilder, Marc; Dugas, Martin ; Albert, Thomas ; Kerl, Kornelius Tobias: Smarcb1 Loss Results in a Deregulation of esBAF Binding and Impacts the Expression of Neurodevelopmental Genes
Inhalt
- Materials and Methods
- Generation of the 81K1 ESC Line
- Cell Culture
- RT-qPCR
- Western Blot
- Co-IP Experiments
- Evaluation of Cell Growth and Cell Viability: MTT Assay and Doubling Time
- RNA-Seq
- ChIP-Seq for Ezh2, H3K27ac and H3K4me3
- ChIP-Seq for Smarca4 and H3K27me3
- Analysis of ChIP-Seq Data—Alignment and Peak Calling
- ChIP-Seq Visualisation in Peak Profiles
- Gene Ontology (GO) Analysis
- Comparison of Smarca4 and Smarcb1 Knockdown Data
- Combining RNA-Seq and ChIP-Seq Data
- Permutation Tests and Antibody Enrichment
- Enhancer Analysis
- Results
- Smarcb1 Regulates Gene Networks Involved in the Development of the Nervous System, Cell Organisation and Adhesion
- The Regulation of Nervous System-Related Genes Is More Dependent on Smarcb1 Than on Smarca4 Function
- Upon Smarcb1 kd, Smarca4 Binding and Histone Marks Change in Gene Regions Connected to Nervous System, Cell Organisation and Adhesion
- A Subset of Downregulated Genes with Smarca4 INCREASE after Smarcb1 kd Show an Unexpected Binding Pattern
- Smarcb1 Loss Results in Changes in Enhancer Occupancy, Particularly in Regions Regulating Nervous System-, Cell Organisation-, Adhesion- and Chromosome Organisation-Related Genes
- Discussion
- Conclusions
- References